The important role of city commercial banks in bank system indicates the importance to enhancing bank corporate governance. Empirical analysis of governance effect on ownership structure of domestic urban commercial banks is conducted by panel data examples of 27 city commercial banks in Jiangsu，Zhejiang，Shandong and Shanghai during 2007—2012 and by stochastic frontier model considering non-efficient term. The research finds that the state-owned attribute characteristics of the biggest shareholder of city commercial banks in example cities are significant，plays an active role in business performance of the city commercial banks but produces passive influence by their centralized-style ownership structure while the business performance of the city commercial banks can be boosted by relatively more efficient ownership supervision and strategic investors. Thus，the future deepening reform of the shareholding system of the city commercial banks should further standardize the shareholding behaviors of the state-owned shareholders， actively introduce strategic investors，make efforts to cultivate rational big shareholders，consolidate ownership supervision in order to realize the transformation from “theoretical supervision” to “practical supervision” in internal governance of the city commercial banks.