In order to reduce economic uncertainty and seek common development, more and more countries, including China, choose to join various regional trade agreements (RTA), which is bound to have a profound impact on China’s participation in the global value chain. This paper constructs the depth of regional trade agreement by longitudinal measurement and calculates the depth of the trade agreement that China participates in and is still in force. Then we analyzed its influence on the participation of manufacturing industry in the global value chain. The results show that the depth of the agreement can improve the forward participation and restrain the backward participation of china in the global value chain. In the heterogeneity analysis, the different RTA types acted in the same direction, consistent with the baseline regression results. In terms of the types of contracting states, the depth effect of agreements between China and developed countries is the same as overall results. In mixed agreements, the depth of the agreement works in the opposite direction. In agreements in which only developing countries were involved, increasing the depth of the agreement would only contribute to backward participation. Among the core clauses, the depth of e-commerce and intellectual property protection clauses can deepen the forward participation and reduce the backward participation in global value chain, which has the greatest impact on improving the embedding position in GVCS.