The proportion of value-added trade among China-ASEAN member countries is gradually increasing. Using the OECD-WTO TIVA input-output database, this paper finds that the value-added trade index of China-ASEAN region increased by 49.7% from 2005 to 2015. During this period, China-ASEAN economic linkage shows a U-shaped trend. The two-way fixed effect and GMM dynamic test show that value-added trade has a significant positive impact on the economic linkage between China and ASEAN, and industrial structure differences have a positive mediating effect on the economic linkage of value-added trade. The greater the difference between the two industrial structures is, the more significant the impact of value-added trade on the economic linkage between China and ASEAN is. Under the background of value chain division of labor, China-ASEAN should give full play to the structural differences and complementary advantages of its members’domestic industries, strengthen the division of labor and cooperation in value chain, and continuously promote regional economic integration.