Based on the shortcomings of academic research and the investment path of high-tech industry innovation capital, this paper puts forward the investment structure of high-tech industry innovation capital, and builds a model of the impact of high-tech industry innovation capital investment structure on innovation efficiency on the basis of theoretical analysis. Based on the panel data of China’s provinces in 2009—2016, the model parameters were estimated. The results show that the high-tech industry innovation capital investment structure has a significant positive non-linear impact on innovation efficiency. The optimal structure for high-tech industry innovation capital investment is 1.79:1. When the innovation capital investment structure is below 1.79, the marginal impact of it on innovation efficiency is 0.680,when the innovation capital investment structure spans 1.79, the marginal impact is reduced to 0.380. Further quantitative attribution analysis found that due to the constraints of high-tech industry innovation level, government support intensity and export intensity, the impact of high-tech industry innovation capital investment structure on innovation efficiency is nonlinear. On the basis of the above analysis, the policy enlightenment of optimizing the investment structure of high-tech industry innovation capital and improving innovation efficiency the paper puts forward.