The four-stage analysis framework of NSUSBM-SFA-NSUSBM-Tobit was constructed in this paper. Based on the cross-section data of 213 cities in China, NSUSBM model was used to calculate the environmental efficiency of cities under the separable and inseparable assumptions. Then the three-stage DEA model was used to introduce natural factors. And combined with the new development concept, The Tobit model was used to analyze the influencing factors of urban environmental efficiency. Research showed, The average urban environmental efficiency in China was 0.49, the overall efficiency was not high, and regional differences were obvious. For some high-quality development cities, the relatively excellent natural environment compensated for the inefficiency of management to a certain extent, and there was still a room for improvement in its management inefficiency. For low-quality cities, the inseparability of GDP and environment pollution were the main causes of environmental inefficiency. Innovation ability had obvious promoting effect on urban environmental efficiency. The proportion of secondary industry was negatively related to environmental efficiency. The greater the difference between urban and rural areas, the lower the environmental efficiency. Government's environmental investment and regulation helped to improve urban environmental efficiency. Opening up and introducing foreign capital had a significant effect on improving urban environmental efficiency. Urbanization helped to improve environmental efficiency.