It is vital to promote and optimize the technological innovation efficiency of new energy vehicle (NEV) enterprises for the green transformation of China’s automobile industry. However, China’s NEV enterprises still have problems such as insufficient research of technology and unreasonable innovative resource allocation. To improve the technological innovation efficiency of China’s NEV enterprises, the NEVs’ technological innovation process is divided into two stages: the research and development (R&D) stage and the achievement transformation stage in this research. Combining Tobit regression with data envelopment analysis (DEA), an evaluation framework of technological innovation efficiency of the NEV enterprises is constructed. Then, the innovation efficiency of 23 NEV listed enterprises from 2013 to 2018 is analyzed. The result reveals three findings. First, the overall technological innovation efficiency of NEV enterprises is low. Second, enterprises’ R&D efficiency is generally higher than the achievement transformation efficiency. Third, according to two-stage efficiency, 23 NEV enterprises are divided into four categories. For different types of enterprises, targeted guidance to improve innovation efficiency is proposed. This research provides a theoretical and practical basis for improving the innovation efficiency of NEV enterprises.