Objective To refrain the medical costs from out-of-control increase, and identify a per-disease payment mode suitable for New-CMS.Methods Case studies were conducted on all the data of five diseases in the course of three years, in a field study of the pilot counties for NRCMS in Anhui Province.Results This system of per-disease "pay by segmentation and quota" is composed of five parts: choice of diseases, measurement of payment criteria, method of settlement, method of compensation, and methods of supervision.Conclusion This system is an effective way to keep the medical costs in the NRCMS under control, given an effective play of the five supportive measures including the clinical pathways for individual diseases.