Based on innovation ecosystem theory and population relationship theory, listed companies in China’s new energy automobile industry are divided into groups of companies in different niches. Based on the qualitative comparative analysis of fuzzy set, the linkage mechanism of business model innovation of new energy automobile enterprise groups in different ecological niches was explored from five dimensions of resource base, entrepreneurship, technological innovation, incentive level and environmental dynamics. The research results show that in the low-niche enterprise population, there are two high-level business model innovation linkage mechanisms of “technical innovation-incentive level” and “technological innovation-environmental dynamics”; in the mid-niche enterprise population, enterprises are mainly driven by internal resource base and entrepreneurial spirit to achieve business model innovation and development; in the high-niche, there are three business model elements linkage mechanisms of “entrepreneurship-environmental dynamics”, “entrepreneurship”, and “incentive level-environmental dynamics”.