Wang Yang, also known as WangKaiyuan, chief China representative of the Linux Professional Institute, jumped onto the stage as Gates was presenting prizes for student innovation.
The Microsoft chief looked on bemused as Wang Yang held up a sign proclaiming 'Free software, open source'.
Zhao Xiaoliang, acting executive of Red Flag Software, said in a comment posted on the Chinese Sohu.com message boards: "I was surprised at Wang's act because we met a couple of times before and he seemed to be a cautious man.
"But I think Wang might have acted for the benefit of China's software buyers."
Red Flag Software aims to provide high quality Linux related products and services in China.
Wang Yang was on stage for 30 seconds before being detained and questioned by police.
"We respect everyone's right of free speech and the incident did not damage Microsoft's innovation event in Peking University," said Chen Ranfeng, a publicity executive for Microsoft China.
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