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Based on the panel data of 30 provinces in China from 2011 to 2019, this paper uses a two-stage DEA model to measure regional innovation efficiency, then non-parametric test is used to examine the impact of innovation network structure and government R&D investment on regional innovation efficiency. The results show that, at the provincial level, innovation efficiency of regional R&D is not necessarily in direct proportion to the innovation efficiency in the commercialization stage. Commercialization efficiency is not necessarily high in provinces with high technical R&D efficiency. At the national level, the innovation efficiency gap between our country’s R&D and commercialization stage is small, indicating that the development of the national innovation efficiency is more and more balanced. Innovation network structure can promote the R&D efficiency, but has no significant effect on the commercialization efficiency. Government R&D investment helps to improve the R&D efficiency, but it is not conducive to the improvement of commercialization efficiency. The interaction between innovation network structure and government R&D investment will have compound effects on regional innovation efficiency; the region with underdeveloped innovation network structure can increase the government R&D investment to make it have a higher level of R&D. This paper provides insights into how to improve innovation efficiency in different social networks and policy environments.