The manufacturing supply chain in China has moved to a new form of innovation ecosystem with a novel characteristic of multi-agent collaboration. According to this new phenomenon, we integrate the ecological niche perspective with the theory of institutional economics to explore the impact mechanism among ecological niche-fitness, collaborative capacity and innovation investment in China's high-tech manufacturing sector. With panel data from 2011 to 2020, our results show a U-shaped nonlinear relationship between ecological niche-fitness and industry innovation scale, and a positive impact of ecological niche-fitness on innovation investment intensity. The economic development level has moderating effects on these relationships, and the association between ecological niche-fitness and innovation investment scale is moderated by collaborative capability. Theoretically, we enrich the innovation literature by incorporating ecological niche-fitness into the context of innovative ecosystem. We also provide important managerial implications for regional governments to regulate innovation ecosystems and promote industrial innovation.