Abstract: The conception of ecosystem has widely considered to be a new model of technology innovation. Multinational enterprises’ worldwide R&D strategies and R&D location have a positive impact on the formation, transformation and evolution of regional independent innovation ecosystem. The paper carries out an investigation about the foreign capital institutes countrywide in China. Tour core categories that can indicate the characteristics of the internal networks, the ecological embeddedness, co-dependence, and co-evolution with regional independent innovation ecosystem are proposed utilizing qualitative research grounded theory with three-steps encoding data. This explores the main path of embeddedness achieved by industrial ecosystem, business ecosystem and culture ecosystem overcoming some constrains. Then a model of co-evolution between foreign capital R&D ecosystem and regional independent innovation ecosystem is designed. It can describe the internal regularities of the doubled-systems’ co-evolution. Suggestions proposed by the paper will help in both the institutes’ management of networks and government’s policies optimal design of regional innovation ecosystem.