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The aim of this research is to investigate China’s urban green total factor productivity (TFP) under the background of progressing urbanization and intensifying environmental pollution, and found out its main influencing factors. In this paper, green TFP of 285 prefecture-level cities in China from 2005 to 2012 was estimated through Malmquist productivity index. Results showed that the annual growth of green TFP in main cities in China is 3.5% and the overall growth declines gradually. Viewed from decomposition of green TFP, technical progress is the main contributor of green TFP growth. Furthermore, the northern coastal region has achieved the highest annual growth of green TFP (4.5%) and the northwest region achieved the lowest growth of green TFP (1.24%), indicating the great regional differences of green TFP and economic growth quality in China. According to analysis on influencing factors of green TFP in main cities, it has been concluded that per-capita urban road area, number of Internet users, proportion of fiscal expenditures, environmental regulation level and technical input are significantly positively correlated with green TFP, while industrial structure and foreign direct investment (FDI) are significantly negatively correlated. Finally, policy suggestions to improve urban green TFP in China were proposed.