As a new industry, the healthy development of new energy vehicle industry is of great significance for effectively solving environmental problems and energy crises. The purpose of this study was to analyze the technological innovation process of China’s new energy vehicle enterprises and construct the evaluation index system of technology innovation efficiency of China’s new energy vehicle enterprises and SBM model-based network DEA model from the two aspects of technology research and development stage and achievement transformation stage. The overall technological innovation efficiency and staged efficiency of 16 listed new energy vehicle enterprises in China were measured and combined with the Malmquist Index Model. The technical change and efficiency change of 16 listed new energy vehicle enterprises in China, spanning from 2012 to 2018, were analyzed. The results show that the average overall efficiency of technological innovation of 16 new energy automobile companies is 0.5515, and the standard deviation is 0.2341. It reflects the low overall efficiency of technological innovation of Chinese new energy vehicle enterprises and the uneven development and the huge gap between different enterprises. From 2012 to 2018, the M index is less than 1, and the technical level change (TC) has a greater negative impact on the M index.