With the aggravation of global climate change and environmental pollution, governments of various countries have taken measures to promote sustainable development. This study evaluates the influence of China's pollutant discharge fees (PFE) on the enterprises' coordinated emissions reduction of pollutant and carbon based on fixed effects model by using a broad sample of 138,371 observations during 2003–2009 derived from two microenterprise datasets and a city dataset. Based on the empirical results, the rising price of PFE will lead to coordinated emissions reduction, specifically, a 1% increase in PFE leads to 0.0835% reduction in SO2 and 0.0294% decrease in CO2. Through heterogeneous analysis, this study finds that PFE heterogeneously influences pollutant and carbon emissions. The collaborative emissions reduction effects of PFE are significant in low pollution intensity regions, high energy consumption intensity regions, and state-owned enterprises. Furthermore, this study concludes that the clean energy substitution effect is an essential mediation mechanism of the impact of PFE on coordinated emissions reduction, while the energy-saving effect is not significant. This study provides several policy implications for achieving the goal of coordinated decreasing the emissions of carbon and pollutant from the perspective of PFE.