How to solve the contradiction between economic growth and ecological environmental protection is a practical problem that should be solved urgently at present. The development of green technology in the manufacturing industry must rely on technology innovation. However, the process of implementing green innovation in the manufacturing industry is full of high uncertainty and risk. First, the green innovation risks were divided into global green R&D risk, global green manufacturing risk, global green marketing risk, and global green service risk from the perspective of the process. Then, this study established a management criteria system of green innovation risk identification in the manufacturing industry under the global value chain (GVC). Furthermore, three methods were applied to identify the green innovation risk of the manufacturing industry under the GVC. Finally, this paper put forward the countermeasures to the green innovation risk of the manufacturing industry under the GVC. The empirical research results of this paper are as follows: From the perspective of the green innovation process, four risks are classified in this study, namely, global green R&D risk, global green manufacturing risk, global green marketing risk, and global green service risk. Among the four stages of green innovation risk, green marketing risk is the highest, followed by green service risk, and green R&D risk and green manufacturing risk are the least. Global green service risk and green R&D risk can be reduced mainly through risk diversification and risk reduction. Global green manufacturing risk and green marketing risk can be reduced mainly through risk diversification and secondary through risk reduction.