Wuyishan City has a long history. Before the Qin (221-206 B.C.) and Han (206 B. C. - 25 A. D.) dynasties, the city was under the jurisdiction of the State of Yue, in Southeast China. According to ancient records and archeological evidence, the site of the city was inhabited more than 4,000 years ago. "Boat-shaped Coffins" suspended from cliffs, said to be some 3,800 years old, can still be seen. After Emperor Qin Shihuang conquered Yue, he set up Minzhong Prefecture, and a city on the site of present-day. Wuyishan was founded as a border city.

In the Later Tang Dynasty (923 - 936 A.D.), the city was put under Jianyang County's administration. In the fifth year of the Chunhua reign period of the Northern Song Dynasty (994), the area was named Chong'an County, and in the Yuan Dynasty (1279-1368), Chong'an County came under the jurisdiction of Jianyang Lu. The area became well-known when the leading philosopher Zhu Xi gave lectures in Ching'an, where he resided for some time. In 1989, Chong'an County was re-named Wuyishan City.