The demonstrators accused the museum of endorsing China's territorial claim over Tibet because the exhibition does not mention the military takeover of the region in the 1950s.
They demanded the museum display the Dalai Lama's portrait and mention China's "invasion" of Tibet at the exhibit.
Museum spokesman Lin Chen-feng flatly rejected both demands.
The exhibition Tibet - Treasures from the Roof of the World, focuses on Tibetan arts and Buddhism, but makes no mention of the Dalai Lama or China's occupation of Tibet.
About 400 Tibetans live in Taiwan, and the Dalai Lama's Tibetan government-in-exile opened a representative office in Taipei in 1998.