The Qing dynasty ruled over the island of Taiwan from 1683 to 1895. The Qing dynasty sent an army led by General Shi Lang to defeat the Ming loyalist Kingdom of Tungning in 1683. Taiwan was then formally annexed in April 1684.

Taiwan was governed as Taiwan Prefecture of Fujian Province until the establishment of Fujian–Taiwan Province in 1887. The Qing dynasty extended its control of Taiwan across the western coast, the western plains, and the northeast over the 18th and 19th centuries. The Qing government did not pursue an active colonization policy and restricted Han migration to Taiwan for the majority of its rule out of fear of rebellion and conflict with the Taiwanese indigenous peoples. Han migrants were barred from settling on indigenous land, and markers were used to delineate the boundaries of settled areas and mountain dwelling aborigines. Despite Qing restrictions, settlers continued to enter Taiwan and push the boundaries of indigenous territory, resulting in the expansion of Qing borders in Taiwan to encompass all of the western plains and the northeast. The lack of state-sponsored colonial administration led to frequent rebellions by Han settlers. By the end of Qing rule in 1895, Taiwan's ethnic Han population had increased by over two million, with some estimates suggesting over three million, making Hans the majority demographic on the island. Taiwan was ceded to the Empire of Japan with the Treaty of Shimonoseki in April 1895, following the Qing dynasty's defeat in the First Sino-Japanese War.

After the defeat of the Kingdom of Tungning at the Battle of Penghu in 1683, the 13-year ruler Zheng Keshuang surrendered to the Qing dynasty. The Kangxi Emperor celebrated the defeat of the Ming loyalist regime in Taiwan which had troubled the Qing for decades. He composed two poems in celebration of the victory. Admiral Shi Lang, who had led Qing forces against the Zheng in naval battle, was awarded a hereditary title, the "Marquis of Sea-Pacification," on 7 October 1683.

Shi Lang remained in Taiwan for 98 days before returning to Fujian on 29 December 1683. His stay in Taiwan made him feel that annexing the island was of greater importance than expected, due to its economic potential. At a conference in Fujian to determine Taiwan's future, some officials from the central government advocated to transport all of Taiwan's inhabitants to the mainland and abandon the island. Prior to 1683, Taiwan was associated with traditional stereotypes of a wild barbarian island beyond the sea. It bore monikers such as the "Island of Dogs" and "Island of Women" or was situated near those places on maps. Kangxi regarded the island as "a ball of mud beyond the pale of civilization" which did not appear on any map of the imperial domain until 1683. Their primary concern was the defeat of the rebels which had already been accomplished. One argued that defending Taiwan was impossible and increasing defense expenditures was highly unfavorable.

Shi, however, vehemently opposed abandoning Taiwan. Yao Qisheng had also been strongly in favor of annexing the island. On 7 October 1683, Yao stated that though Taiwan had not been part of China, the Zhengs had wreaked havoc on the mainland for 20 years after seizing it from the Dutch, and if Taiwan was relinquished, it would once again be occupied by rebels threatening the Chinese coast. Shi argued that to abandon Taiwan would leave it open to other enemies like criminals, adventurers, and the Dutch. He assured that defending Taiwan would not be exorbitant and would only take 10,000 men, while garrisoned forces on the South China coast could be reduced. Shi convinced all the attendees at the Fujian conference, with the exception of the special commissioner from Beijing – Subai – that it was in their best interests to annex Taiwan. On 7 February 1684, Shi sent a memorial to Kangxi with arguments to keep Taiwan, including descriptions of the island's economic products, the cost of relocating Taiwan's inhabitants, and a map of its geography. Prior to the Qing dynasty, China was conceived as a land bound by mountains, rivers and seas. The idea of an island as part of China was unfathomable prior to the Qing frontier expansion effort of the 17th century. With the official inclusion of Taiwan in an imperial map of the Qing dynasty, local officials were instructed to collect information about the island's geography and compile them into a gazetteer. Documentation of Taiwan's geography proceeded in a piecemeal fashion and local officials rarely ventured beyond Taiwan's prefectural capital in the early years. As a result, most of the earliest travel writings were confined to centers of Chinese settlement. Jiang Yuying was put in charge of Taiwan's first draft gazetteer in 1688 and the first official gazetteer was published in 1696.

I have personally traveled through Taiwan and seen firsthand the fertility of its wild lands and the abundance of its natural resources. Both mulberry and field crops can be cultivated; fish and salt spout forth from the sea; the mountains are filled with dense forests of tall trees and thick bamboo; there are sulfur, rattan, sugarcane, deerskins, and all that is needed for daily living. Nothing is lacking .... This is truly a bountifully fertile piece of land and a strategic territory.

— Shi Lang

On 6 March 1684, Kangxi accepted Shi's proposal to set up permanent military establishments in Penghu and Taiwan. The final recommendation for annexing Taiwan was presented on 27 May. It was accepted by Kangxi, who authorized the establishment of Taiwan Prefecture as a new prefecture of Fujian Province, including three counties: Taiwan, Zhuluo, and Fengshan. Yang Wenkui was appointed chief commander of Taiwan.