Firstly, we analyzed China’s agricultural development in last 20 years. Secondly, we pointed out three problems with which China’s agriculture is confronted. (1) The steady increase in costs of agricultural production. (2) The rise of prices of domestic farm products and the increase in imports of foreign agricultural products. (3) The decrease in or stagnation of production of some agricultural products. Thirdly, it was pointed out that agricultural policies of Japan and China have heterogeneity that originated in time lag of the entry into the GATT/WTO, the difference of land ownership system and existence or nonexistence of agricultural cooperatives, though agricultural policies of two countries also have strong homogeneity. Finally, we indicate that three research themes are very important as agricultural economics research cooperation scheme of Japan and China. They are (1) the research on the agricultural management structural reform, (2) the research on the appropriate agricultural protection strategy and (3) the research of the means of improving farmers’ income.