Improving environmental efficiency is a critical way to reduce greenhouse gas such as CO2. However, there is still need for further research on the environmental efficiency of county-level cities, especially the impact of R&D investment. This paper proposes a super slacks based measure model with bad output to analyze the environmental efficiency of 280 county-level cities in China, considering the R&D impact. Next, the panel quantile regression method is adopted to study the factors which influence environmental efficiencies, including industrial structure, GDP per capita, energy consumption per capita, and government net spending. The result shows that most county-level cities in China have a relatively low level of environmental efficiency. The paper also analyzes some factors that can affect environmental efficiency. (1) Industrial structure is a positive factor for the environmental efficiency. (2) GDP per capita is positively correlated with the environmental efficiency. (3) Energy consumption per capita harms the environmental efficiency. (4) The effect of government deficit can decrease the environmental efficiency
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