Historical records show that a temple was originally built in the 17th century as a Chinese-style ancestral shrine in honor of Zheng's father Koxinga.

[4]: 107  The Japanese were perceived as attempting to downplay Koxinga's historical reputation and legacy as a folk hero in order to legitimize their rule of Taiwan.

[5][6] The conversion of the shrine was part of a larger assimilation campaign to advance idea that Taiwan was always separate from China.

In 1942, Miyazaki Naokatsu, governor of Chūreki District in Shinchiku Prefecture, made the argument that Taiwanese mausoleums were Shinto, and when Taiwan became Japanese territory, Taiwanese kami became Japanese kami..[4]: 108 Tainan Shrine was built on the site of the death of Koxinga, a few blocks away from Koxinga Shrine.

Similarly to the Japanese campaign, the Kuomintang government used the shrine as a way to legitimize its rule against the ascendant People's Republic of China across the Taiwan Strait[9] and was visited by Chiang Kai-shek.