Under the constraints of resources and the environment, exploring the channels to improve the quality of China’s economy is very important for China’s current sustainable development. Therefore, this paper studies whether innovation can improve the quality of China’s economy and explore the path of sustainable development from the perspective of the city. Based on the Malmquist–Luenberger index and DEA-Malmquist index, this paper, respectively, measures the green total factor productivity (GTFP) and total factor productivity (TFP) of 193 cities in China. On the basis of obtaining the GTFP, TFP, and various pollutant emissions of 193 cities, this paper selects environmental regulations as the threshold variable and the number of urban patents as the explanatory variable to measure the level of urban innovation. On this basis, we examine the impact of innovation quality on economic quality and environmental pollution under different environmental regulatory intensities. The research results show that the impact of innovation on GTFP and TFP under different environmental regulations is always positive, but the impact coefficient and significance level vary. In addition, the impact of innovation on SO2 emissions under different environmental regulations has also changed. With the increase of environmental regulations, the effect of reducing emissions is gradually significant. The conclusion of this paper better interprets the development of TFP and GTFP under the innovation-driven strategy, provides a decision-making basis for departments at all levels to formulate innovation support policies, and explores the path of sustainable development.