On the basis of the two-stage DEA model, the non-performing loan is introduced as the non-expected output in order to improve the traditional two-stage DEA model.With the new model and the original model to estimate the efficiency of 16 listed commercial banks, this paper makes an analysis on the overall efficiency and sub-stage efficiency and makes a comparison between the deposit-obtaining stage and the profit-gaining stage. The results show that NPLs have a significant influence on bank efficiency;the SOBs are more efficient than the JSBs. The over-all efficiency of banks in China is attributed by the deposit obtaining stage before 2008 and mainly attributed by the second stage after 2008.