Data envelopment analysis(DEA) has been proved to be an excellent approach for measuring of high-tech industry innovation performance, but the existing literatures ignore that enterprises will return the economic benefits of innovation to two-stages for further development and production, so as to ensure continuous innovation. Therefore, this paper combines the characteristics of high-tech industry innovation process into two sub-stages of technology research and development and commercial transformation. A two-stage efficiency measure model considering shared feedback is proposed, which not only extends the DEA methods, but also promotes the research of innovation performance management. The empirical results show that the overall efficiency of Chinese high-tech industries is good, and there is still room for improvement. However, the inter-provincial development is unbalanced, and there are obvious differences in the efficiency of different stages within the provinces. The implementation of targeted management is an effective measure to improve the innovation performance.