How to realize the transformation from high-speed economic growth to high-quality development is an important proposition that needs to be solved urgently in the socialist economy with Chinese characteristics in the new era. The existing theoretical research and practical experience show that innovation-driven is the key breakthrough of the structural reform of supply-side, and effective clustering of innovative elements is a necessary condition to achieve innovation-driven. Thus, from the central government to local governments are vigorously promoting the effective accumulation of innovative elements. Existing research shows that government plays a very important role in the process of government-led innovation, and corruption, as a kind of government behavior that hinders the allocation of resources, may not be conducive to the effective accumulation of innovative elements. Based on this, this paper first introduces corruption into the theoretical analysis framework of innovation factor agglomeration and innovation efficiency. The conclusion of theoretical analysis preliminarily shows that innovation factor agglomeration is conducive to improving innovation efficiency, while administrative corruption inhibits this positive effect. Meanwhile, when anti-corruption efforts are strengthened, this inhibition effect may be eased to some extent. On the basis of theoretical analysis, this paper further uses Tobit spatial panel regression model and IV Tobit model to empirically test the above conclusions based on China's provincial panel data from 2002 to 2016. The empirical results show that the government-led innovation factor agglomeration effectively promotes the improvement of innovation efficiency, while the existence of corruption inhibits this positive effect. The conclusions of this study remain consistent after considering endogenous problems and conducting a series of robustness tests. At the same time, the analysis results of the spatial econometric model show that the spatial spillover effect of innovation factor agglomeration is significantly negative, that is, there is a phenomenon of "separate governance" among regions, indicating the lack of regional collaborative innovation. Further research found that the strengthening of anti-corruption efforts after the 18th National Congress of the Communist Party of China has effectively alleviated the negative effects caused by corruption, and also corrected the negative spatial spillover effects of the concentration of innovation elements, indicating that the anti-corruption actions after the 18th National Congress released the system dividend for the "innovation driven strategy", and provided a living soil conducive to the effective concentration and allocation of innovation elements. The above findings have certain reference value for the path choice of high-quality economic development in the new development stage of China. Therefore, this paper argues that the innovation inhibition effect of corruption means that strengthening anti-corruption efforts and streamlining administration and delegating power can improve the institutional environment of innovation factor agglomeration. Notably, although anti-corruption can reduce the incentive to seek political connection and improve innovation efficiency, the distortion of market mechanism is the root cause. Therefore, we should handle the relationship between the government and the market well, transform the functions of the government, further improve the market mechanism, and finally form a model of innovation element gathering that focuses on market allocation and is supplemented by government guidance.