During the years of Qayamat Se Qayamat Tak, Khan married Reena Dutta. They had two children, a son named Junaid and a daughter, Ira. 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 does not attend any Indian film award ceremony as he feels "Indian film awards lack credibility".

In 2007, Khan lost a custody battle for his younger brother Faisal to their father, Tahir Hussain.

In 2007, Khan was invited to have a wax imitation of himself put on display at Madame Tussauds in London. However, Khan 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, "

Gandhiji

is one person who inspires me!