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At the beginning of the Qing Dynasty, Taiwan was a prefecture under the jurisdiction of Fujian province and included three counties, Jhuluo, Taiwan and Fongshan. The Tainan County today belonged to the two counties of Taiwan and Jhuluo. In 1885, Taiwan was upgraded to a province, with Taiwan Prefecture renamed Tainan Prefecture. During the Japanese Occupation, Tainan Prefecture was changed to Tainan County in March 1896, and again to Tainan Sub-Prefecture in November 1901. Almost twenty years later in 1920, the region was renamed Tainan Jhou (a division under the prefecture), and after Taiwan's Retrocession in August 1945, the two cities in Tainan Jhou, Tainan and Chiayi, were established as provincial cities in November, with the remaining ten counties and 65 townships forming Tainan County.

Tainan County Government was established on January 7, 1946, governing “districts” instead of “counties,” and siang or jhen became the terms used to denote townships. Later, the two townships of Shueishang and Taibao were redrawn as parts of Chiayi City, Anshun Township was redrawn as a part of Tainan City, and four townships, Lin’nei, Mailiao, Baojhong and Dongshi were set up anew, with the Alishan Aboriginal Territory changing to Wufong Township. At this point, the jurisdiction of Tainan County included 10 districts with 15 jhens, 52 siangs (townships), 1,166 villages, and 15,649 neighborhoods. On April 9 of the same year, the government relocated from Tainan to the present address in Sinying. On October 25, 1950, after the administrative districts were redrawn, the jurisdiction of Tainan County included only five of the original districts, which were, Sinying, Sinhua, Sinfong, Beimen, and Zengwun, with seven jhens, 24 siangs (townships), 499 villages, and 6,901 neighborhoods. 

On February 2, 1968, Syuejia Siang was upgraded to Syuejia Jhen. On December 25, 1981, the seat of Tainan County Government, Sinying Township, was changed to Sinying City. Later, in light of its rapid increase in population, and according to Article 7-2 of the Implementation Outlines of Local Governance for Townships and Cities in Taiwan Province, townships with a population of over 150,000 may be established as a county municipality, Yongkang Township was upgraded to Yongkang City on May 1, 1993. After the latest adjustment (March 1999), Tainan County today includes two cities, seven jhens, 22 siangs (townships), 521 villages, and 9,638 neighborhoods.