In the process of China’s transformation from high-speed to high-quality development, the role of green innovation has gradually begun to receive attention. Using 2163 observations of 687 listed companies from 2016 to 2020, this paper examined whether green innovation can improve green economic efficiency. The study found that green innovation significantly reduces the green economic efficiency of enterprises. In the case of insufficient protection of innovation achievements, limited knowledge and technology accumulation, and the absence of enterprise engagement in heavily polluting production and operation activities, the negative impact of green innovation on their green economic efficiency is more significant. Moreover, upgraded production processes, a high degree of freedom of technology selection and high market competition can help alleviate the negative impact of green innovation on enterprises’ green economic efficiency, and when the above three conditions are simultaneously met, green innovation significantly promotes the green economic efficiency of enterprises. The above findings are contradictory to the assumption of most literature intuitively. However, after a series of tests, this paper found that green innovation can still stimulate overall environmental and economic performance in some conditions. Starting from the microenterprise level and based on actual emissions data, this paper examines whether and how green innovation affects high-quality development. The findings are of great significance to academic research, policy formulation, and enterprise production and operation.