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The former boxing world champion, 35, said he and his wife Faryal were robbed at gunpoint by two men in Leyton earlier this week.
Khan criticised the London mayor for failing to tackle crime in the capital, urging him to “pull his finger out”.
Speaking at a St George’s Day event in Trafalgar Square, Sadiq Khan told the PA news agency: “He’s in my thoughts, it must have been really scary for him.
“What’s really important is of course, if anybody knows anything about who robbed Amir Khan of his watch, they contact the police or contact Crimestoppers anonymously.
“It’s no consolation to Amir Khan that violent crime has been going down in our city over the last few years.”
He added: “I understand he was petrified, he was scared, it’s really important to understand and have empathy with the victims of crime.
“As the mayor I speak to victims of crime on a regular basis and it is really distressing when you’ve been robbed and I understand his anger, I understand his fear.”
The Metropolitan Police has asked the public for any information about the “easily” recognisable custom-made Franck Muller timepiece.
Officers were called at just after 9pm on Monday to High Road.
They said no shots were fired and nobody was injured in the attack.
Khan, the former WBA and IBF light-welterweight champion, had told MailOnline: “My plan was to move to London later this year with Faryal and the kids but after what happened there’s no chance that we’ll be doing that.
London is not a place I want to live in anymore.
“Our plan to move there is not happening.”
He also spoke of his anger following the incident.