The museum traces its origins to October 24, 1908, when the colonial government of Japan established the Taiwan Governor Museum to commemorate the inauguration of the island's North-South Railway. In its initial form, the museum collected over 10,000 items -- natural history specimens, ethnographic artifacts, geological samples -- cataloging the colony for its rulers with the systematic thoroughness that characterized Japanese imperial administration. A grander permanent building opened in 1915 in what was then called Taihoku New Park, and it quickly became one of the most prominent public buildings of the colonial period. By 1935, it served as the First Cultural Pavilion at the Taiwan Exposition, a lavish event marking forty years of Japanese rule.

Japan's surrender in 1945 set off a chain of administrative upheavals that the museum absorbed without relocating. The Taiwan Provincial Government took over in 1949 and renamed it the Taiwan Provincial Museum. Renovations in 1961 and 1994 updated its facilities but preserved its neoclassical shell. When Taiwan restructured its government in 1999, the museum transferred to central government administration and received its current name. In 1998, the Ministry of the Interior declared it a National Heritage site -- an official acknowledgment that the building itself, not just its contents, merited preservation. It remains the only museum established during the Japanese colonial period still operating on its original site, a distinction that speaks to both the building's resilience and the community's attachment to it.

In 2005, a government project began knitting the National Taiwan Museum together with surrounding historical buildings into a unified Capital Museums System. The network now includes four distinct venues: the museum itself, the Land Bank Exhibition Hall housed in a former Nippon Kangyo Bank building and designated as a natural history museum, Nanmen Park occupying the old Monopoly Bureau camphor factory with exhibits on Taiwan's industrial history, and Railway Department Park on the site of the colonial-era transportation administration. Additional buildings -- including the former Mitsui Bussan Company headquarters -- are slated for future restoration. Together, they form a constellation of repurposed colonial architecture, each building carrying the DNA of Japanese-era Taipei into the present.

The museum maintains five departments -- anthropology, earth sciences, zoology, botany, and education -- organized around the premise that understanding Taiwan requires understanding the land itself. Permanent exhibitions cover the island's prehistory and its indigenous cultures, while outdoor displays include bronze buffalo sculptures, stone tablets, relics of a megalithic culture, old cannons, and vintage locomotives. A major exhibition titled "Exploring Taiwan," opened in February 2021, brings together over 300 cultural and historical items divided into two narratives: People of Taiwan and Nature of Taiwan. The museum sits a short walk northwest from NTU Hospital Station on the Taipei Metro, making it one of the most accessible introductions to the island's deep history.