From the micro-enterprise level, this paper analyzes the relationship between the capital allocation efficiency of new energy vehicle enterprises and vehicle carbon emissions with technological innovation as the threshold variable. The results are as follows: Firstly, Whether R&D investment, R&D personnel input or patent is used to measure technological innovation, there is a double threshold effect between capital allocation efficiency and vehicle carbon emissions. When R&D investment intensity, R&D personnel input intensity or the ratio of patent number to R&D personnel is at a low level, the improvement of capital allocation efficiency will significantly increase vehicle carbon emissions. When the level of R&D investment intensity, R&D personnel input intensity or the ratio of patent number to R&D personnel exceeds the first threshold of 2.981, 13.7, 6.67, the promotion of capital allocation efficiency on vehicle carbon emissions will be weakened. When the level of R&D investment intensity, R&D personnel input intensity or the ratio of patent number to R&D personnel exceeds the higher threshold of 5.837, 19.6, 10.80, the positive externality of capital allocation efficiency is highlighted, which promotes the reduction of vehicle carbon emissions. Secondly, compared with R&D personnel input and patents, R&D investment has a greater impact on the relationship between capital allocation efficiency and vehicle carbon emissions. Thirdly, the technological innovation has a certain accumulation effect. Fourthly, government support and free cash flow will restrain vehicle carbon emissions, while energy intensity, debt constraint and enterprise size will increase vehicle carbon emissions.