Based on the perspective of innovation value chain, this paper constructs the evaluation system of scientific and technological innovation efficiency of industrial enterprises above scale in China, measures the efficiency of scientific and technological innovation of 36 industrial subdivision industries by using DEA-Tobit model and studies its influencing factors. The results show that: the industrial enterprises above the scale of scientific and technological innovation efficiency of the industry gap is very significant, the average comprehensive efficiency of R&D stage is only 0.38, pure technical efficiency is the main cause of the low overall efficiency; the average comprehensive efficiency of the transformation stage is 0.83, the efficiency of pure technology and scale restrict the improvement of overall efficiency. In the analysis of the factors influencing the efficiency of scientific and technological innovation, it is found that more investment is not as good as possible, and it is very important to allocate resources reasonably according to the characteristics of the industry. Based on the results of empirical analysis, this paper puts forward the relevant countermeasures and suggestions.