Abstract: By constructing an innovative input-output model, it is found that the innovation efficiency of China's manufacturing industry is steadily increasing, fluctuating up and down, and gradually decreasing. On this basis, the M-index decomposition of innovation efficiency was further found. Except for Fujian, Hainan and Qinghai, the total factor efficiency index of other provinces increased steadily, and the induced factors showed regional characteristics. Finally, establish a regression model of innovation efficiency affecting economic growth, and find that the improvement of innovation efficiency has a crowding out effect on economic growth. Combined with the analysis results of the M-index model and the regression model, it is proposed to improve the innovation efficiency from the aspects of optimizing the structure of innovation elements, constructing an innovative collaboration platform and improving the innovation value chain.