Objective: Through evaluating the creadit level appraisal of designated medical institutions under new rural cooperative medical system ( NCMS) , effective method of standard management for NCMS designated medical institutions under was proposed. Methods:Use third-party evaluation to evaluate the 27 NCMS designed medical institutions in Jiangsu, divide the results into groups and make a comparative analysis based on the relevant properties of rated agencies. Results: Compared to 2011, the credit level appraisal on NCMS medical institutions in Jiangsu is higher in 2012; the score of public medical institutions, medical institutions with inpatient department and the general hospitals are higher. The relevant indexes of correlation have significant difference, P≤0.05. Conclusion:Some low-credit medical institutions have disordered charge and over-increasing medical cost. The medical service management needs to be completed. It needs to further implement the management system of NCMS, discover more efficient payment of NCMS, enhance the supervision on private medical institutions, improve the introduction and training of talents and promote the standard and method of evaluation, so as to improve the sustainable development of NCMS.