Abstract: A modified three-stage DEA model that can eliminate the influence of environmental variables and random errors is used to empirically analyze the operating efficiency of the city commercial banks in China from three aspects, namely technique, pure technique and scale efficiencies. Meanwhile, by comparing the efficiency of the state-owned and nationwide listed joint stock banks with that of the city commercial banks, the efficiency variation feature of the last one between the year of 2006~2010 is highlighted. The results show that the efficiency of city commercial banks is much lower than that of the other two kinds and the difference mainly comes from scale efficiency, which may provide a reference to the decision makers for deciding the business policy and improving the management strategy.