With the establishment and development of China-ASEAN Free Trade Area, agricultural trade between China and ASEAN is developing rapidly and is increasingly close. Based on the HS92 six-digit data of China’s agricultural exports to the ASEAN market from 2000 to 2015, and combined with enterprise heterogeneity theory, the research shows the value of intensive margin is less than extensive margin, but the contribution rate of intensive margin is higher than extensive margin. The empirical results show that the influencing degree of each variable on intensive and extensive margin is different. The impact of trade costs and the relative productivity of binary margin are negative, the relative GDP of the importing country, the scale of the agricultural economy and the financial crisis have a positive effect on the intensive margin of China’s agricultural exports to the ASEAN market, but have a negative effect on the extensive margin.