Objective: To evaluate the degree of systematic innovation in the health system，and promote the formation of long-term and unique competitive advantages in the health industry. Methods: A synergetic model of health industry innovation ecosystem is built combining with ecological concepts. Empirical analysis is conducted on the data from 2009 to 2020 is used for. Results: The result shows that the degree of synergy in the health industry innovation system is low. In terms of the order degree of subsystems，the order degree of innovation production subsystem，innovation application subsystem and innovation environment subsystem generally show an upward trend，while the order degree of innovation integration subsystem fluctuates obviously. Conclusion: It is suggested to improve the synergy of China's health industry innovation ecosystem by strengthening biological components，optimizing non-biological components and promoting the coordinated development of the system.