Medals and awards sold for 296,750 pounds ($387,708), compared with an estimate of 15,000 pounds, while the red motorised wheelchair sold for 296,750 pounds ($387,708), also compared with an estimate of 15,000 pounds.
The copy, one of only five originals of the thesis entitled "Properties of expanding universes", smashed pre-sale expectations four times over to sell for £584,750 at the Christie s sale, which ended on Thursday.
The history-making PhD thesis is signed twice by Prof Hawking and was inscribed by the scientist in the year he was diagnosed with motor neurone disease.
The wheelchair raised $387,480 (£296,750), nearly 20 times more than pre-auction estimates of up to $19,500 (£15,000).
The most expensive item in Hawking's collection was a copy of his Ph.D. dissertation on the expansion of the universe. His doctors gave him just two years to live, and the devastating news led him to lose hope and quit his studies.
Among the items was Hawking's motorized wheelchair, used in the 1980s and 1990s.
Some of his belongings including essays, medals, awards and a copy of his book a "Brief History of Time" signed with a thumbprint were sold online alongside letters and manuscripts belonging to Isaac Newton, Charles Darwin and Albert Einstein.
Image: This Simpsons script - an episode that featured Professor Hawking - sold for £6,250.
Stephen Hawking was born on 8 January 1942 in Oxford. "A small plastic model of his yellow Simpsons incarnation had pride of place in his house".
"We are very pleased to have the assistance of Christie's to help us with the important matter of managing our beloved father's archives and his unique and precious collection of personal and professional belongings, chronicling his life and work", said his daughter Lucy Hawking in a statement before the lot took place.