The global and domestic divisions of labor have had a great influence on the economy and environment in China during the last decade. With the refinement of production processes, national value chains (NVCs) coexist with global value chains (GVCs), enabling regions to participate in dual value chains (DVCs) simultaneously. This study calculates the NVCs and GVCs participation of manufacturing sectors in China’s provinces. On this basis, this research adopts a fixed effects model to analyze the impact of GVCs and NVCs participation and their interaction effect on manufacturing upgrades and green development. The results show, first, that significant regional differences in GVCs participation exist among provinces in China. In comparison, provincial NVCs participation demonstrates fewer regional differences. Second, there are significant sectoral differences of GVCs participation in China’s manufacturing industry—high-tech manufacturing is more embedded than other manufacturing industries. The sectoral differences in NVCs participation are relatively small. Third, GVCs and NVCs participation and their interaction effect have significantly promoted the upgrading and green development of manufacturing sectors in provinces of China, and this impact exhibits significant heterogeneity across regions, industries, and NVCs participation modes. The conclusions of this study provide empirical evidence and policy recommendations for the upgrading and green development of China’s manufacturing industry.