As an effective means of addressing environmental externalities, market-based environmental regulation inevitably has potential effects on the economy. Based on Porter’s theory, we investigate how emission charges affect firms’ total factor productivity and explore the moderating role of firms’ breakthrough technological innovation. Our findings reveal the moderating effect of breakthrough technological innovation on the total factor productivity enhancement of the emission fee by looking at Chinese A-share listed firms with heavy pollution from 2011 to 2020. Our mechanism tests suggest that emission fees and breakthrough technological innovation increase firms’ total factor productivity by enhancing firms’ green innovation. In addition, our heterogeneity analysis shows that emission charges and breakthrough technology innovation effectively increase total factor productivity only for state-owned firms, and the effect on total factor productivity of non-state-owned firms is insignificant. Our findings suggest that implementing market-based environmental regulations and incentives for firms to embark on breakthrough technological innovation effectively increases firms’ total factor productivity.