Following the spirit of Fukuyama and Weber (2010) and Chen et al. (2010), this paper proposes a linear two-stage network system model with shared inputs and undesirable outputs, to analyze the technical efficiencies of Taiwanese banking industry over the period 2004-2013. As compared to the conventional DEA approach, the extended model is able to deal with the problem of shared inputs and intermediates among activities which characterize bank production in an integrated framework simultaneously, and allow us to examine aspects of production in a more comprehensive and factual manner. The results show that the average system technical efficiency score over the sample period is 0.896, suggesting that there is a 10.4% room for FCUs to improve their efficiency. The decomposition indicates that the average efficiency in phase 1 is 0.821 and that of phase 2 is 0.958, signifying that the efforts to improve inputs utilization efficiency in phase 1 are more important than efforts to improve loan and investment creation and problem loan control efficiencies in phase 2. It is also found that the 2008 financial crisis and the European Debt Crisis did not have significantly impacts on the performances of domestic banks. The comparisons of the performances of different groups of banks demonstrate that the banks with mixed private-public-ownership perform better than the private banks, and the financial holding banks are superior to independent banks which suggest that joining financial holding companies would create potential synergies and helps to enhance banks’ competitiveness. In addition, production scale is a positive influential factor for banks’ performance which indicates that more effort is needed to increase the scale of Taiwanese banking to make progress.