The main purpose of this article is to analyze the relation between the formation of the official indigenous education policy in the early period of Japanese colony and the report “The History and Custom of Taiwan Indigenous Peoples ". “The History and Custom of Taiwan Indigenous Peoples “was the official report for the Chief of the Civil Affairs, Goto Shinpei, by two officials of Department of Civil Affairs, Ino Kanori and Suo Chuanji. The purpose of survey was the preparations for educating indigenous peoples. Most part of this report was based on field study, which could help to see education from an anthropological perspective. For establishing an education system for indigenous peoples, it divided to the different levels of civilization of each different ethnic group of indigenous peoples, and then gave each an appropriate education. Comparing the subsequent development of the indigenous education system that Taiwan Governor’s Office of Japanese initiated, it found there were some similarity and difference between the official report and the practical policy. The reason for the difference based on the development of indigenous educational policy that was different from the educational unit in the indigenous areas under the jurisdiction of the developmental department.