Taoyuan Martyrs Shrine was first built by the Japanese as a Jinja. Before the 918 incident, the Japanese government did not take an active role to establishing Jinja in Taiwan. At that time, there was only 25 Jinjas in Taiwan. When the Japanese government started preparing for war in 1931, the colonial government promoted the campaign of "one Jinja for each village" in an effort to promote Jinja as the spiritual center in Taiwan.

On September 23, 1938 (the13th year of the Showa Era), the founding ceremony of Taoyuan Jinja was held to worship the three Gods of Creation and Prince Nohisa, as well as the Harvest God and the Meiji Emperor. This Jinja then became affiliated with the entire county during the last years of the war, and then with Hsinchu. The structure is divided into a main section, ceremonial hall, administration office, and hand washing area. It has a streamlined shape, evidenced particularly in the curved roof. Pilgrims must wash their hands with a bamboo ladle before they proceed to the ceremonial hall, in order to cleanse themselves symbolically of the impurities of earthly existence.

Pilgrims worship gods in the ceremonial hall. The gods' tablets are located here, along with a donation box and bell. To maintain the sanctity of the hall, only master worshippers are permitted inside during ceremonies. The monks manage daily affairs from the administration office.

There were about 200 Jinjas built in Taiwan during Japanese occupation. After Taiwan and Japan severed official relations, the government announced the "Rules regarding removal of Japanese Imperialism's superiority from the memorial remains in Taiwan" to tear down all Jinjas in Taiwan. Taoyuan Jinja was the only one unaffected. Its fine shape, superior construction materials, and elegant structure attract people. This building was classified as grade three ancient site on February 15, 1994.