This study aims to understand whether the banks' joining the financial holding companies would promote their operating efficiency. This paper uses a sample of 14 banks under financial holding company and 33 independent banks by making the comparison of their operating efficiency, and utilizes the data envelopment analysis, as input orientated is the subject, to analyze the technical, pure technical and scale efficiency by employing the CCR and BCC models. Furthermore, we use Malmquist Productivity Index to evaluate the trend of productivity change, and employ the Tobit regression method to examine the exogenous impact on efficiency. The results suggest that the banks under financial holding company perform better than independent banks in terms of technical, pure technical, and scale efficiency. With regard to the resource allocation and utilization, improvement of administrative skills, and product innovation, the banks under financial holding company outperform independent banks