Objective In order to improve the health food laws, regulations and management measures, enhance the uniformity and professionalism of health food supervision, promote the healthy and orderly development of the health food industry. Methods This paper combed the specific method of Japanese health functional food management through literature research, expert discussion and enterprise research. Results It could be seen that Japanese health functional foods were divided into three categories:specific health foods, functional label foods and nutritious functional foods. Different categories adopted different product approval models, and some raw materials have achieved standardized management. Conclusion The ingredient of health functional foods in Japan were managed by different classifications of products. At the same time, the practice of enterprises undertaking the main responsibility has certain implications for the management of ingredient for health foods in China.