To establish the evaluation index system of urbanization innovation level and ecological efficiency, the entropy method is applied to measure the comprehensive index of urbanization innovation level and ecological efficiency, the VAR model is established, and empirical measurement is used to study the internal relationship and dynamic development between urbanization innovation level and ecological efficiency. The empirical results show the following: (1) The overall development of the innovation level in 30 cities in China is uneven, there is a large gap between the urban innovation level in backwards areas and economically developed areas, and there is a certain coupling effect between the urban innovation level and ecological efficiency. (2) There is a long-term dynamic equilibrium relationship between the urban innovation level and ecological efficiency, which will exert certain pressure on the ecological environment in the process of urbanization. However, the continuous improvement of urbanization will have a positive impact on the improvement of the ecological environment. (3) The improvement of ecological efficiency will also promote the improvement of the urban innovation level. Therefore, this paper puts forwards policy suggestions to promote the harmonious development of urbanization and the ecological environment and provides a reference for realizing the balanced development of urbanization and ecological efficiency in China.