Japan is the largest export destination for Chinese agricultural products. The export status to Japan is directly related to the overall trend of China’s agricultural exports. Based on the HS9-coded agricultural product trade data of the Japanese Ministry of Finance in 2001- 2017, using the ternary marginal analysis method, the driving force of China’s agricultural exports to Japan was analyzed in this paper from a static and dynamic perspective. The results showed that 98.89% of the driving force of China’s agricultural exports to Japan was from the contribution of quantity margin. The contribution of the extensive margin had been decreasing year by year after 2006, and it has been negative for many years. The reason was that technical barriers such as the Positive List System lead to less export of agricultural product in varieties and types. The average marginal contribution rate of price was 8.26%. The average price of exported agricultural products has been basically higher than the world average level since 2013, suggesting that the quality of exported agricultural products has been improved. While maintaining the quantity of agricultural exports, improving the quality of agricultural products, expanding export varieties and increasing export value added are the sources of sustainable growth of China’s agricultural exports in the future.