This article utilizes the DESTA and EORA databases to develop indicators for bilateral value chain cooperation and systematically explores the relationship between value chain cooperation and the depth of regional trade agreements. The findings indicate that deepening value chain cooperation substantially encourages the establishment of more comprehensive regional trade agreements, particularly between countries with strained bilateral political relations, considerable institutional differences, and more extensive trade cooperation in intermediate goods. The results remain robust even after addressing potential biases, omitted variables, and reverse causality. Mechanism tests suggest that deeper value chain cooperation results in the accumulation of institutional frictions, which in turn fosters the deepening of regional trade agreement terms, thereby significantly reducing non-tariff trade costs. This study offers both empirical and theoretical insights for countries pursuing deeper trade cooperation and contributes to the development of a global trade governance framework.