Promoting agricultural development from a green perspective is an important direction for realizing the modernization of agriculture and rural areas. Since the 1970s, a green development model for agriculture has gradually formed in Japan, with organic agriculture and environmentally friendly agriculture as the main paths. Japan has achieved certain results in system construction, policy support, identification of ecological farmers, reduction of chemical input, and other aspects by undertaking several measures, such as the innovation of organization, establishment of a sound legal system, and reinforcement of the guiding role of excellent cases. The inductive method was applied in this study to systematically determine the innovation of relevant organizations and evolution of the legal and regulatory system of green agricultural development in Japan. Additionally, the case study method was used to summarize and compare the successful paths and main experiences of some excellent cases. We found that, first, a coordinated promotion mechanism of integrating officials and citizens has gradually formed in Japan upon the establishment of social groups, parliamentarian unions, organic societies, and other organizations. Second, a more accurate support system for laws and regulations has gradually been built by competent administrative departments under the continuous improvement of relevant policies to support the green development of agriculture. Meanwhile, various honors with Japanese characteristics have been set by the Competent Departments of Agriculture and Forestry in Japan to encourage farmers and agricultural business organizations to choose green production behavior; many excellent farmers and agricultural organizations have emerged and they play a good demonstration and leading role in the green and sustainable development of agriculture in Japan. However, the overall scale of organic and environmentally friendly agriculture in Japan remains a niche industry for the national agricultural layout. Although the penetration rate of environmentally friendly agriculture has increased considerably, Japan still faces some realistic challenges, such as the decreasing number of ecological farming households, limited premium space for green agricultural products, and relatively small scale and certification area of organic agriculture. To cope with these challenges, Japan has made great efforts to cultivate new agricultural business entities and actively promote the international development of organic agriculture. In addition, Japan has explored many innovation paths, such as creating regional environmental symbiotic industrial chains based on the idea of “integration of production and consumption”. Based on these results, the following suggestions are put forward for green and high-quality agricultural development in China: first, clarifying the path for green agricultural development and establishing technical standards for the reduction of chemical inputs; second, formulating an identification system for ecological farmers and cultivating successors to green agricultural development; third, attaching importance to the social academic groups for giving full play of their roles and functions to create a legal environment for green development of agriculture; fourth, building a national unified market for green agricultural products based on those products with good quality and based on the idea of “local production for local consumption”.