Upon arriving in San Jose, Thornton improved the Sharks' fortunes and found instant chemistry with winger Jonathan Cheechoo.
During the absence of usual alternate captain Alyn McCauley from the San Jose line-up, Thornton donned the "A" for the first time as a Shark in a game against the Phoenix Coyotes on March 30, 2006, and wore the "A" whenever McCauley was out of the line-up for the remainder of the season.
Tallying 92 points in 58 games with the Sharks after the trade, Thornton finished the season with a league-leading 96 assists and 125 points total to earn the Art Ross Trophy as the league's top scorer.
He became the first player to win the award while splitting the season between two teams.
Due to Thornton's success, Cheechoo also enjoyed a career-season, winning the Rocket Richard Trophy as the NHL's top goal-scorer with 56 goals.
However, in the 2006 playoffs, Thornton was once again criticized for his play, as his production decreased to 2 goals and 9 points in 11 games as the Sharks were ousted in the second round.
In the off-season, Thornton was honoured for his regular season play and was awarded the Hart Memorial Trophy as the league' regular season MVP to go with his Art Ross Trophy.
He is the only player in NHL history to win the Hart Trophy while playing for two different teams in the same season.

Thornton began the 2006–07 season being awarded a permanent alternate captaincy, but struggled in the first half of the season while suffering from a toe injury that did not heal until January 2007.
After recovering, Thornton enjoyed a productive second half, battling Pittsburgh Penguins Sidney Crosby for a second-consecutive scoring title late in the year, eventually finishing six points behind Crosby with 114.
With a league-leading 92 assists, Thornton became only the third player in NHL history to record back-to-back 90-assist seasons, joining Wayne Gretzky and Mario Lemieux.

Thornton began the 2007 playoffs by recording six assists in the Sharks' first-round series against the Nashville Predators.
Advancing to the second round against the Detroit Red Wings, he recorded a goal and three assists in the first three games of the series.
However, Thornton was effectively neutralized by Red Wings defenceman Nicklas Lidström, for the remainder of the series as the Sharks were eliminated in six games.

In the off-season, Thornton signed a three-year contract extension worth US$21.6 million that kept him with the Sharks until June 2011.
In the 2007–08 season, Thornton finished with 96 points (29 goals and 67 assists) to finish fifth in NHL scoring.
In 2008–09, Thornton was named captain of the Western Conference for the 2009 NHL All-Star Game in Montreal.
He completed the season with 86 points.
In the subsequent playoffs, he recorded a goal and four assists in six games as the Sharks were eliminated in the first round by the Anaheim Ducks.

 
In September 2009, before the start of the 2009–10 season, the Sharks acquired Dany Heatley in a three-player trade that sent Thornton's struggling former linemate Jonathan Cheechoo, left-winger Milan Michalek and a second-round draft pick to the Ottawa Senators.
Thornton, Heatley, and Sharks captain Patrick Marleau were joined on the Sharks' top line and enjoyed immediate offensive success together.
The trio helped the Sharks to one of their best-ever regular seasons in franchise history.
Although the line's production slowed down in the second half of the season, all three Sharks players finished in the League's top 15 in point-scoring.
Thornton's 89 points ranked eighth, while Marleau and Heatley finished 14th and 15th in League scoring with 83 and 82 points, respectively.
The Sharks entered the 2010 playoffs as the first seed in the Western Conference for the second-consecutive year.
After advancing past the Colorado Avalanche and Detroit Red Wings in the first two rounds, the Sharks were eliminated by the Chicago Blackhawks in the Western Conference Finals.
Thornton finished the playoffs with a career-high 12 points in 15 games.

After the elimination, team management vacated
Upon arriving in San Jose, Thornton improved the Sharks' fortunes and found instant chemistry with winger Jonathan Cheechoo. During the absence of usual alternate captain Alyn McCauley from the San Jose line-up, Thornton donned the "A" for the first time as a Shark in a game against the Phoenix Coyotes on March 30, 2006, and wore the "A" whenever McCauley was out of the line-up for the remainder of the season. Tallying 92 points in 58 games with the Sharks after the trade, Thornton finished the season with a league-leading 96 assists and 125 points total to earn the Art Ross Trophy as the league's top scorer. He became the first player to win the award while splitting the season between two teams. Due to Thornton's success, Cheechoo also enjoyed a career-season, winning the Rocket Richard Trophy as the NHL's top goal-scorer with 56 goals. However, in the 2006 playoffs, Thornton was once again criticized for his play, as his production decreased to 2 goals and 9 points in 11 games as the Sharks were ousted in the second round. In the off-season, Thornton was honoured for his regular season play and was awarded the Hart Memorial Trophy as the league' regular season MVP to go with his Art Ross Trophy. He is the only player in NHL history to win the Hart Trophy while playing for two different teams in the same season.
Thornton began the 2006–07 season being awarded a permanent alternate captaincy, but struggled in the first half of the season while suffering from a toe injury that did not heal until January 2007. After recovering, Thornton enjoyed a productive second half, battling Pittsburgh Penguins Sidney Crosby for a second-consecutive scoring title late in the year, eventually finishing six points behind Crosby with 114. With a league-leading 92 assists, Thornton became only the third player in NHL history to record back-to-back 90-assist seasons, joining Wayne Gretzky and Mario Lemieux.
Thornton began the 2007 playoffs by recording six assists in the Sharks' first-round series against the Nashville Predators. Advancing to the second round against the Detroit Red Wings, he recorded a goal and three assists in the first three games of the series. However, Thornton was effectively neutralized by Red Wings defenceman Nicklas Lidström, for the remainder of the series as the Sharks were eliminated in six games.
In the off-season, Thornton signed a three-year contract extension worth US$21.6 million that kept him with the Sharks until June 2011. In the 2007–08 season, Thornton finished with 96 points (29 goals and 67 assists) to finish fifth in NHL scoring. In 2008–09, Thornton was named captain of the Western Conference for the 2009 NHL All-Star Game in Montreal. He completed the season with 86 points. In the subsequent playoffs, he recorded a goal and four assists in six games as the Sharks were eliminated in the first round by the Anaheim Ducks.
 
In September 2009, before the start of the 2009–10 season, the Sharks acquired Dany Heatley in a three-player trade that sent Thornton's struggling former linemate Jonathan Cheechoo, left-winger Milan Michalek and a second-round draft pick to the Ottawa Senators. Thornton, Heatley, and Sharks captain Patrick Marleau were joined on the Sharks' top line and enjoyed immediate offensive success together. The trio helped the Sharks to one of their best-ever regular seasons in franchise history. Although the line's production slowed down in the second half of the season, all three Sharks players finished in the League's top 15 in point-scoring. Thornton's 89 points ranked eighth, while Marleau and Heatley finished 14th and 15th in League scoring with 83 and 82 points, respectively. The Sharks entered the 2010 playoffs as the first seed in the Western Conference for the second-consecutive year. After advancing past the Colorado Avalanche and Detroit Red Wings in the first two rounds, the Sharks were eliminated by the Chicago Blackhawks in the Western Conference Finals. Thornton finished the playoffs with a career-high 12 points in 15 games.
After the elimination, team management vacated
Joe Thornton