A motorised wheelchair that belonged to the physicist, who died in March and which was expected to fetch £15,000, went for nearly £300,000.
When Cambridge finally made Hawking's thesis available to download in 2017, it was viewed more than 60,000 times in 24 hours and public interest completely crashed the university's server.
Diagnosed with motor neuron disease at 22 and given just a few years to live, Hawking instead died in March at 76.
Those items included a black bomber jacket, the script from an episode of The Simpsons on which he appeared and a 1988 copy of his best-selling book, A Brief History of Time, marked with his thumbprint as a signature.
Hawking's 117-page dissertation "Properties of expanding universes" from 1965 sold for 584,750 pounds ($764,024) well ahead of the estimate of up to 150,000 pounds. Along with inclusion of Hawking's personal belongings, the auction also included belongings linked to scientists including Isaac Newton, Charles Darwin and Albert Einstein, wrote The Guardian.
Hawking's daughter Lucy said that the sale gave "admirers of his work the chance to acquire a memento of our father's extraordinary life in the shape of a small selection of evocative and fascinating items".
The sale, run online by Christie's and including 52 lots, raised more than £1.8m on Thursday.
The auction funds will go to the family although the money raised from selling the wheelchair will be donated to the Motor Neurone Disease Association and the Stephen Hawking Foundation.
Hawking's children hope to preserve his scientific archive for the nation.