How to utilize human, financial, and material resources reasonably in the technological innovation of new energy vehicles to obtain the maximum benefit with the least investment is an important issue that needs to be solved urgently. This paper employs the stochastic frontier model to analyze the innovation efficiency and its influencing factors of new energy vehicles in China. The investment of innovation is divided into four dimensions: human resource input, R&D input, technology acquirement input and environment support input. The results demonstrate that the mean of innovation efficiency of the new energy vehicle industry is low in general. The Yangtze River Delta and Pearl River Delta regions have the highest innovation efficiency comparable to that of other regions. There is a significant positive impact of asset turnover ratio, per capita compensation of management, and education level on innovation efficiency. The effects of asset-liability ratio and government support on innovation efficiency are not significant. But the government support has a significant positive moderation effect on innovation efficiency through financial factors. Based on the conclusions, this paper proposes insights to promote the development of the new energy vehicle industry.

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