Abstract: Under the cross background of innovation becoming the first driving force of development and innovation resource constraints, there is great significance to improve the efficiency of industrial R&D for the realization of industrial innovation and development. Break through the limitations of single-stage or two-stage research on industrial R&D efficiency, this paper introduces GVC into the evaluation system of industrial R&D efficiency, and constructs the three-stage evaluation system of industrial R&D efficiency based on the deconstruction of GVC from two aspects of embedding potential and embedding intensity; on this basis, empirical research on the R&D efficiency of China's high-end equipment manufacturing industry is conducted based on the three-stage perspective and SFA method, this paper reveals the law of three-stage R&D efficiency and their influencing factors. The results show that: (1) the embedding potential of GVC of the empirical industry is gradually increasing, but the embedding intensity is relatively stable; (2) the three-stage R&D efficiency of the empirical industry rises steadily in the empirical period, and the efficiency of R&D direct output is the highest, the climbing efficiency of GVC is the lowest; (3) the influencing intensity, significance and direction of the R&D input factors and influencing factors are heterogeneous. Based on the achievements of the empirical research, this paper puts forward the strategies to improve the industrial R&D efficiency, such as "strengthening GVC embedding" and "promoting the development of private sectors".