Chemical fertilizer plays a very important role in promoting agricultural production and food security. However, currently the amount of fertilizer used is too large and the utilization efficiency of fertilizer is low. As a result, chemical fertilizer has become a major source of agricultural pollution. In order to coordinate the relationship between agricultural development and environmental protection, China and Japan have carried out a series of studies on efficient fertilization and environmental assessment since 1997-2016. This paper reviews the main research achievements of the 20 years of Sino-Japanese cooperation, expounds the main achievements and revelations of the 20 years of cooperation, and puts forward some thoughts and suggestions for future cooperation. It suggests some new ideas for Sino-Japanese cooperation in future with high quality production and environmental protection in agriculture in mind.