Conjoined mode is a great significance to promote the formation of good medical order during the reform of public hospitals. What aspects should the Medical Association pay attention to in the economic operation management, so as to ensure the effective operation? Value chain management is a kind of management method appearing in the end of last century. We can use this management to analyze the industrial chain of medical industry and the internal decomposition of Medical Association, and we can tap the value of operation, promote the stable and orderly operation of Medical Association, and promote the formation of core competitiveness of hospital. Therefore, this paper discusses the application of value chain management in economic management under different modes of medical alliance