Abstract: Under the driving force of digital innovation, the ecological competition trend of emerging industries is deepening. Building emerging industry innovation ecosystems and conducting scientific and effective strategic management is of great significance to enhance the international competitiveness of China’s industries. However, the existing strategic management theories lack sufficient attention to China’s industrial context and digital context. Based on the comprehensive advantage theory, this study takes China’s new energy vehicle industry as a longitudinal case and explores the formation mechanism of the comprehensive advantage of emerging industry innovation ecosystem. The results show that: (1) the ecosystem experiences the three evolution stages of digital innovation “competence storage period – empowerment periods – competence expansion period”, and has formed the comprehensive advantages with different characteristics through “strategic change – strategic upgrading – strategic transition” at each evolution stage; (2) in terms of the driving forces and strategic paths, the formation of the comprehensive advantage is driven collectively by China’s unique institutional, technological and market contexts, and develops cyclically along the strategic paths of “dominant advantage selection – core competence cultivation – comprehensive advantage formation”; (3) accompanied with the dynamic selection of dominant advantages between “digital resources – digital platforms – digital ecosystems”, the ecosystem has cultivated the core competence of “distributed innovation competence”, “recombination innovation competence” and “cross-border integration innovation competence” in turn, and has promoted the synchronous formation and continuous evolution of comprehensive advantage manifested in a “multi-point breakthrough – platform empowerment – ecological integration” overall trend. Based on the above conclusions, this study finally constructs the theoretical framework of the formation mechanism of the comprehensive advantage of emerging industrial innovation ecosystem. Meanwhile, considering that the industrial digital reformation is still in a dynamic wave, future research should continue to track the strategic changes of emerging industries and refine a new round of comprehensive advantage strategy cycle, thus improving the theoretical framework with higher contextual adaptability and strategic guidance value. In terms of the theoretical contributions, this study helps to facilitate the cross integration of multiple theoretical fields, enrich the competitive strategy research of innovation ecosystems at the industry-level, advance the indigenous strategic management theories in the digital context, and realize the multi-dimensional expansion of the comprehensive advantage theory at the levels of “enterprise – cluster – industry – industry innovation ecosystem”. In a practical sense, this study may provide three aspects of implications for China’s digital innovation practice, industrial strategic planning, and policy system optimization. First, the industrial management departments should implement differentiated comprehensive advantage strategies according to the specific types of emerging industries. The three strategic paths revealed in this study may provide valuable reference for the strategic planning of emerging industries in different regions, industrial types and evolution stages. Second, innovative enterprises, as core members of the emerging industry innovation ecosystem, should take advantage of the digital resource endowment and platform empowerment to accelerate the cooperation and integrated innovation with more digital ecological partners. Third, the government should speed up the construction of the digital innovation policy system, and enhance the complementarity, context adaptability and process coherence of the innovation policy mixes.