He married 29-year-old Hadia Sher Ali, a Pakistani descendant from Afghan royalty, in a lavish ceremony in Pakistan last year.
Whether she found it impossible to follow in the Princess's formidable footsteps as his lover, or whether Diana cast a shadow over their relationship even in death, he will not say."I got married in May 2006 but separated recently - in November [last year]," he says.
She stayed at his central London home, and he at her apartment in Kensington Palace.
The Khans are deeply religious, and his wall-hangings include a painting that has an inscription of verses from the Koran.
Dr Khan, who left Britain last November, pursued his relationship with Diana from 1995.
She even went to Pakistan to speak to Jemima Khan about life there.
However, after a while she no longer talked about Pakistan and although she did not actually say so, Hasnat Khan got the impression that she no longer considered living there a possibility."Dr Khan also revealed to the inquiry that, at the end of 1996, Diana asked Paul Burrell, the former royal servant, to talk to a priest about them marrying in secret.
He speaks tenderly about why he will never divulge the details of his affair with the Princess.
Other lovers, notably former Household Cavalry officer James Hewitt, may have cashed in on their relationship, but the intimate moments Dr Khan enjoyed with Diana will never be shared with a wider audience."Generally I do not talk about people - family or friends. "I'm loyal to her [the Princess] not because she was a celebrity but because I'm loyal to all my friends.
It is understood that at one point the Princess was so smitten with Dr Khan that she contemplated converting to Islam so they could marry.
Yet she abandoned the idea when he decided their relationship could not work in the long term.
These days Dr Khan spends most of his time working as a surgeon in Malaysia.
When he is in Pakistan, he lives in his own spacious yet modestly decorated colonial-style house in Jehlum, the arid central Punjab district that is a two-hour drive from the Pakistani capital of Islamabad.
The surgeon told officers that the Princess had considered moving to Pakistan after he had told her it was the "only way he could see them having any sort of a normal life together".