During the years of Qayamat Se Qayamat Tak, Khan married Reena Dutta. His parents did not approve of their marriage because of her not being a Muslim. As a result, Khan's marriage stayed a secret both from his parents and the media for a while. Dutta made a brief appearance in the popular song sequence Papa Kehte Hain in Qayamat Se Qayamat Tak. The story of Khan's marriage garnered major public attention when it was first revealed. Even so, Reena Dutta maintained a low profile and continued her job at a travel agency. They had two children, a son named Junaid and a daughter, Ira, and led a quiet family life away from the public eye. Reena was involved, briefly, in Khan's career when she worked as a producer for Lagaan. In December 2002, Khan filed for divorce, ending the 15-year marriage, with Reena taking the custody of both their children. On December 28, 2005, he married Kiran Rao who had been an assistant director to Ashutosh Gowariker during the filming of Lagaan.
Though nominated many times, Khan doesn't attend any Indian film award ceremony as he feels &Indian film awards lack credibility
In 2007, his brother Faisal caused a media scandal by accusing Khan of mistreating him and forcing him to take medication. Faisal has been said to be mentally unstable. On October 31, 2007, the Bombay high court granted temporary custody of Faisal to their father, Tahir Hussain. Khan's family came out in a public statement, supporting him on all counts in this matter. The statement was also signed by his former wife, Reena Dutta
In 2007, Khan was invited to have a wax imitation of himself put on display at Madame Tussauds in London.[ However, Khan politely declined stating that, It's not important to me... people will see my films if they want to. Also, I cannot deal with so many things, I have bandwidth only for that much
In a 2009 interview, Khan states that he tends to take an independent approach to the world of filmmaking, noting that he does not "do different things; I try to do it in a different manner. I think every person should follow his/her dream and try and make it possible to create an ability to achieve it backed by its practicality." He has also indicated that he is more interested in the process of filmmaking than in the end result: "For me, the process is more important, more joyful. I would like to have my entire concentration on the process right from the first step When asked about his role model, he stated that, andhiji is one person who inspires me!