In the intercourse of economic and trade process between China and Japan, Farm produce trade conflicts have been always“A Stumbling Block”to disturbed the further development of the relationship in economic and trade affairs between the two countries. Although japan is the country with disadvantages in international competition of agriculture, it’s attitude towards the question of protect their own agricultural products market were exceptional strong, China as a giant of yield agricultural products and trade it with other countries, there is no doubt, the agricultural products markets of Japan a have an intense attraction to China, but the trade barriers which set by Japan keep the Chinese agricultural products out from the market. Therefore, How to avoided the trade barriers, to eliminated and abated the agricultural trade conflicts between China and Japan is the key factor to fulfill the free trade between china and japan。This article through analysing the case of agricultural conflict between China and Japan ,understanding the affect of conflict,want to avoid the agricultural conflict and deepen the agricultural trade cooperative jobs between the three countries.