This study focuses on the factors affecting the financial performance of pharmaceutical manufacturing enterprises. Based on dynamic capability theory and ambidextrous innovation theory, this study adopts the Resource–Behavior–Performance framework to investigate how green supply chain integration (GSCI) and ambidextrous green innovation affect financial performance. The proposed hypotheses were tested through structural equation modeling using data from 400 China’s pharmaceutical manufacturing enterprises. The results indicate that the various dimensions of GSCI and ambidextrous green innovation yield distinct outcomes. Among the three dimensions of GSCI, only green supplier integration and green customer integration significantly impact financial performance directly, unlike green internal integration. Among the two dimensions of ambidextrous green innovation, only exploitative green innovation significantly influences financial performance, acting as a mediator between the GSCI dimensions and financial performance, while exploratory green innovation does not. The main advantages of this study include considering the connotation and value of GSCI from a green dynamic capability perspective, as well as the effects of exploratory and exploitative green innovation as intermediary behaviors while simultaneously considering the performance effects of GSCI and ambidextrous green innovation. This study offers novel academic insights and practical guidelines for pharmaceutical manufacturing enterprises to integrate GSCI and ambidextrous green innovation, with the aim of achieving better financial performance in their sustainable development efforts.