When the Qing wrested the island from the control of the Kingdom of Tungning in 1683, Taiwan was made a prefecture under the administration of Fujian Province. The new prefecture consisted of three counties:
The aboriginal lands on the east coastknown to the Qing as the "Land Behind the Mountains" were not controlled at all, although they were vaguely claimed as part of the empire. The seat of government, also known as "Taiwan" or "Taiwanfu", was located in modern-day Tainan, "which city had been in turn the capital of the Dutch, Koxinga, and the Chinese".
1723–1875
During this period, Taiwan was administered as three counties and two subprefectures. The counties were, from south to north:
Fongshan County: one town, 8 Chinese villages, 73 uncivilized native villages, 8 civilized native villages
Kagi County: one town, 4 Chinese villages, 22 uncivilized native villages, 8 civilized native villages
Tamsui Subprefecture: one town, 132 farms, 70 native villages
1875–1887
An administrative change occurred in 1875, when Imperial CommissionerShen Pao-chen demanded that another prefecture be added in Taiwan to revamp the administrative organization of the northern area of the island. As a result, Taipeh Prefecture was created from part of Taiwan Prefecture.
1887–1895
was established in 1887, consisting of four prefectures: Taipeh, Taiwan, Tainan, and Taitung. Tainan Prefecture was created from part of Taiwan Prefecture. Thus Taiwan Prefecture was reduced to the area of central Taiwan only, composed of the modern-day Miaoli County, Taichung City, Nantou County, Changhua County, and Yunlin County. The new prefecture was divided into four counties and one subprefecture:, Changhua County, Yunlin County, Miaoli County, and. The new prefecture seat was located at the central city of Toatun, which was also designated as the site of the new provincial capital, taking its name as Taiwanfu or Taiwan. However, during construction of the new capital, the provincial capital was temporarily relocated to the city of Taipeh. One of the administrators of Taiwan Prefecture was Raymund Tu, a native priest of Taiwan. Four years after development of Toatun began, the seat of Taipeh was officially declared the provincial capital. In 1895, with the Treaty of Shimonoseki and the successfulJapanese invasion of Taiwan, Taiwan Prefecture was abolished. Under Japanese rule, the province was abolished in favor of Japanese-style divisions.