The excavations that preceded the museum's construction revealed multiple archaeological sites layered beneath the Tainan plain. Among them: the Nanguanli Site, which yielded the remains of dogs that once lived alongside prehistoric communities; the Sampauchu Site, where pig bones testified to early animal husbandry; and the Youhsianfang Site, where rice seeds — preserved across millennia — spoke to the agricultural practices of people who had been farming this ground long before the first Chinese or Dutch settlers arrived. These were not isolated finds but overlapping windows into successive cultures that called southwestern Taiwan home, each building on or alongside what came before.

The irony of the museum's location inside a functioning science park is deliberate. The Southern Taiwan Science Park is one of Taiwan's major technology corridors, home to semiconductor fabrication and advanced manufacturing. The Museum of Archaeology, spanning 24,000 square meters, sits within this landscape as a statement: that understanding where a society comes from is not separate from what it builds next. The branch is affiliated with the National Museum of Prehistory, headquartered in Taitung on Taiwan's eastern coast, which has long been Taiwan's primary institution for Austronesian and prehistoric research. The Tainan branch extends that work directly to the southwestern plains where some of Taiwan's most significant early cultures emerged.

When Vice Culture Minister Lee Lien-chuan attended the soft opening on 26 December 2018, he was joined by a group of Siraya people — and that presence carried weight. The Siraya are a Taiwanese Plains indigenous people whose ancestral lands cover much of the southwestern Tainan plain, the same terrain the museum's collections document. For centuries, the Siraya faced displacement, cultural suppression, and official non-recognition; Taiwan's government did not formally recognize the Siraya as an indigenous people for much of the twentieth century. Their presence at the museum's opening — at an institution dedicated to preserving the prehistoric record of their homeland — was a moment that carried both historical and political significance, acknowledging a continuity of people across the millennia the museum spans.

What the museum ultimately holds is not just a collection of artifacts but an argument: that the Tainan plain has been home to complex human communities for an extraordinarily long time, and that those communities matter to understanding Taiwan's identity. The artifacts displayed range from prehistoric ceramics and stone tools to the organic remains — animal bones, plant seeds — that survived in the archaeological layers. Together they chart the transition from hunter-gatherer ways to settled agriculture, from small village life to the more complex societies that eventually encountered Dutch traders and Qing settlers. The museum makes these transitions visible and tangible, in a building walkable from Nanke Station.