According to the thought of system theory, regional innovation ecosystem consists of four subsystems: the subsystem of regional innovation resources, the subsystem of innovation resources flow, the subsystem of basic environment for innovation, the subsystem of policy environment for innovation. The evaluation index system is established to reflect the diversity of innovation agents, the flow of innovation resource, and the complexity of innovation environmental that highlighting the policy environment for innovation. Improved G1 method based on grey relational degree, the coordination degree model based on bull’s-eye distance and the contribution algorithm of grey target are jointly applied to analyze coordinated development degree of innovation ecosystem for China’s 30 provinces, autonomous regions and municipalities in 2016, and identify the key influencing factors of coordinated development. The results show that the coordinated development level of regional innovation ecosystem is not so high, and presents the obviously spatial pattern of east highest and west lowest. Nationwide, the subsystem of regional innovation resources is the most weak and unbalanced-development subsystem, the subsystem of innovation resources flow is the last but one subsystem. Talent resources, technology flow, fund flow, firm agglomeration condition, legal policy are the important influencing factors of coordination development.