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 was divided into two distinct stages: technology achievement production and technology achievement transformation. By employing the Super-DEA and Malmquist index models, the two-stage innovation efficiency, innovation patterns, and dynamic trends of firms with varying ownership structures from 2016 to 2022 were quantified. 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. The research findings provide theoretical references and policy insights for enhancing the technological innovation efficiency and market competitiveness of the new energy vehicle industry and promoting the high-quality synergistic development of the new energy vehicle industry chain.