will having a different academic name than official name hurt? My academic name school+B.Sc. is Rajesh without a surname, and in passport and all other docs it is Rajesh Lobhani that has the surname. I live in India and wish to work and do phd in Australia. 

Doing M.Sc. currently so do I change my name(for M.Sc) or let it be? The procedure involves changing Xth and XII standard school name, and it very difficult.
Many academics have had multiple names because of marriage, immigration, or other changes. I don't anticipate this being a problem in your case. As AndreasBlass suggested in the comments, just mention it in your application materials somewhere.