The environment is the common property of all human beings, and all should enjoy equal rights to use the environment. Years of growth have greatly improved China's overall economic development, but the problem of environmental inequality has become prominent. Based on data from 278 prefecture-level cities, the Williamson coefficient is used to measure the environmental inequality and environmental pollution-inequality indices of 25 regions from 2003 to 2015, and the effects of the stringency of environmental policy instruments on environmental inequality are discussed. The results demonstrate that the provincial environmental inequalities in China between 2003 and 2015 declined at first and then rose, thus showing a U-shaped trend, and the heterogeneity of various pollutant emissions is substantial. The extent of public participation is negatively correlated with environmental inequality, while the stringencies of command-and-control and market-based instruments are positively correlated with environmental inequality. An inequality process may be necessary during the transformation from a high-pollution to a low-pollution state, so governments should mix a variety of environmental policy instruments to narrow or even eliminate regional environmental inequality. The findings of this study have important implications for the government to effectively choose policy instruments, improve policymaking ability, and eliminate environmental inequality.