Objective：To analyze the trend of the development and operational efficiency of public specialized hospital and private specialized hospital in Guangdong. Methods: Using the Malmquist index model of DEA to analyze operational efficiency of public specialized hospital and private specialized hospital in Guangdong from 2009 to 2015. Results: 2009-2015, The operation efficiency of specialized hospital overall be in low condition；The operational efficiency of public specialized hospital is better than private specialized hospital’s. Conclusion: Medical and health reform policy should attaches great importance to the construction of specialized subject hospital; Private specialized hospital is the cornucopia of hospital development which needs accurate and professional.