This paper is a systematic and in-depth investigation on the process of the official religious policy and its legalization of the imperial. Japan's colonial rule in Taiwan since Japan's occupation of Taiwan in 1895 until the fourth Taiwan governor-general Kodama Gentaroo. The methodology is to use the legal concept of modern western public administration law to examine the then Japan's official religious administrative process. The official archives used are the recently translated manuscripts of Taiwan governor-general office. Therefore, the proof is the most powerful. On the other hand, this paper re-arrange and interpret the census data by "First Division of Temporary Taiwan Old Customs Survey Society" and relevant explanations in consulting with other historical materials and research result. This is to reveal the then important academic achievements which have been neglected by the academic circle. This will definitely help the understanding of the process of Taiwan's contemporary religious legalization.