Abstract: Under the background of global trade liberalization, it is of great significance to explore its impact on China’s agricultural exports from the perspective of trade facilitation to enhance China’s agricultural export competitiveness. This study selected the panel data of agricultural products exports between China and 10 ASEAN countries from 2010 to 2019 and established four primary indicators such as infrastructure, customs environment, regulatory environment, and e-commerce, as well as aviation infrastructure, customs procedures, and 17 secondary indicators such as policy transparency are used to construct the evaluation index system of trade facilitation. The article used the extended gravity model to analyze the primary influencing factors of trade facilitation empirically. The results showed obvious differences in trade facilitation among ASEAN countries, and there was still much room for improvement. The infrastructure efficiency, customs environment, and regulatory environment in the primary indicators of trade facilitation in ASEAN had a significant positive effect on agricultural exports. In contrast, e-commerce had no significant impact on China’s agricultural exports. Based on the empirical results, the study proposed that ASEAN trading countries should strengthen infrastructure construction, optimize the construction of customs and institutional environment, and improve domestic Internet technology and penetration rate from the perspective of development indicators of trade facilitation to promote the improvement of their trade facilitation level. At the same time, it also put forward from the perspective of China that different development countermeasures should be taken for countries with different development levels of ASEAN trade facilitation in order to promote China’s agricultural exports.