The health of urban innovation ecosystems is crucial for smart and modern city construction. Considering the characteristics and formation mechanism of urban innovation ecosystems, an index system of health evaluation for smart cities is established. The combined DEMATEL-TOPSIS method was used to comprehensively evaluate the health of the innovation ecosystem in Wuhan from 2012 to 2020. Moreover, the cause-and-effect relationships among the indicators and the key impact factors are analyzed. The results show that per capita GDP, the number of users with fixed Internet broadband access, and road area per capita are the critical factors influencing the health status of urban innovation ecosystems. The centrality degrees are 1.640, 1.406, and 1.326, respectively, and the causality degrees are 1.264, 0.934, and 0.808, respectively. Through the analysis of closeness coefficients, it can be concluded that the health status of the innovation ecosystem in Wuhan is good and steadily increasing. Finally, policy recommendations for the health development of Wuhan’s innovation ecosystem are proposed.