Abstract: City commercial bank is the product of modern finance and regional economic development. Compared with the traditional commercial banks, the city commercial bank are flexible, strong and innovative. However, due to the short development time, there are some problems in the management and risk control of the city commercial banks. This paper, from the perspective of risk management, regional restrictions and industrial dependence, uses SBM-Undesirable model and Bootstrap rectification technique to estimate the operating efficiency and characteristics of China's 54 city commercial banks from 2010–2014. It is found that there exists stage positive correlation between city commercial bank operating efficiency and its level of risk management; city commercial bank operating efficiency has strong dependence on local industries; cross regional business is conducive to the optimized allocation of city commercial bank resources, and it can achieve the improvement of operating efficiency.