The main purpose of this article is to inquire the development and content of hygiene education in the indigenous educational institution in Japanese colonial period. For Taiwan indigenous peoples, ’’hygiene’’ may be a new concept from Japanese colonizers, which was quite different from the traditional view of ’’clean body’’. The ’’hygiene’’ referred to here was not unique to the Japanese. Japanese acquired ’’hygiene’’ from Western world in the modernization process. This article finds that the children’s hygiene of indigenous educational institution was part of the hygiene training outside the curriculum to establish personal hygiene habits before the revision of the ’’Education Standards for Educational Institution’’ in 1941. After the revision of the ’’Education Standards for Educational Institution’’ in 1941, hygiene was part of physical education. In addition to the basic training of hygiene, hygiene teaching should also be accompanied by first-aid and care.