He married Princess Regina of Saxe-Meiningen on 10 May 1951 at the Church of Saint-François-des-Cordeliers in Nancy, capital city of Lorraine.
The wedding was attended by his mother, Empress Zita.
He returned there with his wife for their golden jubilee in 2001.
Otto lived in retirement at the Villa Austria in Pöcking near Starnberg, upon Starnberger See, Upper Bavaria, Bavaria, Germany.

At the time of his death in 2011, the couple had seven children, 22 grandchildren and two great-grandchildren:
Andrea von Habsburg (born 30 May 1953), married Hereditary Count Karl Eugen von Neipperg (born 20 October 1951 in Schwaigern).
They have three sons and two daughters.
One of them, Dominik, married Marie-Anna, Princess of Salm-Salm, a descentant of Friedrich, Prince of Waldeck and Pyrmont and his wife Princess Bathildis of Schaumburg-Lippe.

Monika von Habsburg (born 13 September 1954), married Luis María Gonzaga de Casanova-Cárdenas y Barón, Duke of Santangelo and Grandee of Spain (born 24 April 1950 in Madrid), son of Balthasar de Casanova-Cárdenas y de Ferrer and María de los Dolores Barón y Osorio de Moscoso, Duchess de Maqueda, a descendant of Infanta Luisa Teresa of Spain, Duchess of Sessa, and sister of Francis, King-Consort of Spain.
They have four sons.

Michaela von Habsburg (born 13 September 1954, twin of Monika), married firstly Eric Alba-Teran d'Antin (21 May 1920 in Mexico City – 9 July 2004 in New York City), and secondly Count Hubertus von Kageneck (born 10 August 1940 in Wittlich), son of Count Franz Joseph von Kageneck and Princess Elisabeth Maria of Bavaria.
Twice divorced, she has two sons and one daughter from her first marriage.

Gabriela von Habsburg (born 14 October 1956), married Christian Meister (born 1 September 1954 in Starnberg).
Divorced in 1997, they had one son and two daughters.

Walburga von Habsburg (born 5 October 1958), married Count Archibald Douglas (born 27 November 1949 in Stockholm).
They have one son.

Karl von Habsburg (born 11 January 1961), married Baroness Francesca Thyssen-Bornemisza (born 7 June 1958 in Lausanne), daughter of Baron Hans Heinrich Thyssen-Bornemisza and Fiona Frances Elaine Campbell-Walter.
They have one son and two daughters.

Georg von Habsburg (born 16 December 1964), married Duchess Eilika of Oldenburg (born 22 August 1972 in Bad Segeberg).
They have one son and two daughters.
He married Princess Regina of Saxe-Meiningen on 10 May 1951 at the Church of Saint-François-des-Cordeliers in Nancy, capital city of Lorraine. The wedding was attended by his mother, Empress Zita. He returned there with his wife for their golden jubilee in 2001. Otto lived in retirement at the Villa Austria in Pöcking near Starnberg, upon Starnberger See, Upper Bavaria, Bavaria, Germany.
At the time of his death in 2011, the couple had seven children, 22 grandchildren and two great-grandchildren:
Andrea von Habsburg (born 30 May 1953), married Hereditary Count Karl Eugen von Neipperg (born 20 October 1951 in Schwaigern). They have three sons and two daughters. One of them, Dominik, married Marie-Anna, Princess of Salm-Salm, a descentant of Friedrich, Prince of Waldeck and Pyrmont and his wife Princess Bathildis of Schaumburg-Lippe.
Monika von Habsburg (born 13 September 1954), married Luis María Gonzaga de Casanova-Cárdenas y Barón, Duke of Santangelo and Grandee of Spain (born 24 April 1950 in Madrid), son of Balthasar de Casanova-Cárdenas y de Ferrer and María de los Dolores Barón y Osorio de Moscoso, Duchess de Maqueda, a descendant of Infanta Luisa Teresa of Spain, Duchess of Sessa, and sister of Francis, King-Consort of Spain. They have four sons.
Michaela von Habsburg (born 13 September 1954, twin of Monika), married firstly Eric Alba-Teran d'Antin (21 May 1920 in Mexico City – 9 July 2004 in New York City), and secondly Count Hubertus von Kageneck (born 10 August 1940 in Wittlich), son of Count Franz Joseph von Kageneck and Princess Elisabeth Maria of Bavaria. Twice divorced, she has two sons and one daughter from her first marriage.
Gabriela von Habsburg (born 14 October 1956), married Christian Meister (born 1 September 1954 in Starnberg). Divorced in 1997, they had one son and two daughters.
Walburga von Habsburg (born 5 October 1958), married Count Archibald Douglas (born 27 November 1949 in Stockholm). They have one son.
Karl von Habsburg (born 11 January 1961), married Baroness Francesca Thyssen-Bornemisza (born 7 June 1958 in Lausanne), daughter of Baron Hans Heinrich Thyssen-Bornemisza and Fiona Frances Elaine Campbell-Walter. They have one son and two daughters.
Georg von Habsburg (born 16 December 1964), married Duchess Eilika of Oldenburg (born 22 August 1972 in Bad Segeberg). They have one son and two daughters.
Otto von Habsburg