This study proposes a two-stage approach to perform metafrontier analysis of the pollution efficiency of administrative regions in Taiwan during 2004–2015. The empirical research shows that New Taipei City and Taipei City have the best performances in terms of metafrontier efficiency and the technology gap ratio. In addition, the average score for pollution efficiency in municipalities is higher than that in non-municipalities for three environmental management indices. However, the metropolitan and non-metropolitan regions face different environmental problems in that the former should pay attention to sewage treatment, while the latter should focus attention on preventing air pollution. Finally, Taiwan presents disparity in the environmental technology gap ratio between these two types of regions.