Based on the content of organic agriculture, sustainable management of agriculture in Japan is analyzed from four aspects. Firstly, organization and management institutions and relevant laws and regulations of organic agriculture in Japan are introduced. Secondly, certification procedure of organic agricultural products is briefly described, that is, determining production plan, reorganizing cultivation and management records, making certification application, on-site inspection, offering certification, and professional work after certification. Thirdly, management of organic agriculture in Japan is analyzed; and the six principal forms of organic agriculture in Japan are summarized. The four basic characteristics of agricultural product circulation and consumption are summed up, which are paying attention to food safety, encouraging residence allocation and dispatch, promoting order production and marketing, and strengthening the communication between production and marketing. Fourthly, operation mechanism of organic agriculture in Japan is introduced, especially the Producer – Consumer "Guidance and Help" System. According to the investigation on the national differences between China and Japan, enlightenment of organic agriculture to China is put forward, including the change of ideas and concepts, the establishment of network organic agricultural association, and the improvement of management system for organic agricultural products.