The development of the new energy vehicle (NEV) industry in China is a strategic endeavor towards green development. As a technology-intensive industry, innovation is pivotal for the NEV industry to advance its high-quality development. From the innovation value chain perspective, the technological innovation process of the NEV industry is divided into two distinct stages: technology achievement production and technology achievement transformation. By employing the Super-DEA and Malmquist index models, this study quantifies the two-stage innovation efficiency, innovation patterns, and dynamic trends of firms with varying ownership structures from 2016 to 2022. The results show that: Firstly, the innovation efficiency in both stages of the NEV industry is generally low, with the majority of firms adhering to an extensive innovation model. However, the efficiency in the technology achievement transformation stage significantly is better than that in the production stage. Secondly, there exists notable heterogeneity in technological innovation efficiency across firms with different ownership structures and within distinct segments of the industrial chain. Specifically, non-state-owned enterprises demonstrate higher technology production efficiency compared to state-owned enterprises, albeit with relatively lower technology transformation efficiency. Additionally, there are more pronounced disparities in technology production efficiency among various segments of the industrial chain. Lastly, from a dynamic perspective, total factor productivity (TFP) in both the production and transformation stages exhibits fluctuating trends, with technical efficiency change and technical change serving as the primary catalyst for TFP growth in different stages respectively. This study offers three aspects of practical guidance for the high-quality development of the new energy automobile industry: revealing the technological innovation efficiency and key growth-promoting factors at different stages of the innovation value chain, guiding enterprises to optimize the allocation of technological innovation resources; analyzing the differences in the innovation efficiency of new energy automobile enterprises with different property rights, and helping the government accurately implement differentiated incentive policies; addressing the weak links in the industrial chain through technological innovation and comprehensively enhancing the innovation tenacity of upstream and downstream enterprises.