Objective: The chief aim of this paper is to explore the characteristics of medical treatment for NCMS inpatients in the central district of the southern city, and identify the main problems, so as to give some suggestions on the promotion of linkage mechanism between medical insurance and hierarchical medical system in the southern city. Methods: Hospitalization person-times and expenses were analyzed using the medical insurance inpatients who have settled in the NCMS information management system in the central district of the sourthen city from 2013 to 2015. Results: Among pieces of data, there were identical 5 system diseases hospitalized both in local and non-local medical institutions from 2013 to 2015: respiratory system diseases, malignant neoplasms, digestive system diseases, genitourinary system diseases, and circulatory system diseases, which also ranked top 5. In the hospitalization ratio of the top 5 systemic diseases in 2015, the respiratory system accounted for the largest proportion of 95.65%, and malignant neoplasms inpatients occupied the largest proportion who hospitalized in non-local medical institutions(36.27%). The proportion of inpatients with genitourinary system diseases hospitalized in non-local medical institutions was higher(10.32%), and the cost was lower(21.44%), compared with that of inpatients with digestive system diseases and circulatory system diseases. We chose the 3 repesentive system diseases to analyze diseases structure: there were 4 diseases of respiratory system diseases, 7 diseases of malignant neoplasms, 3 diseases of genitourinary system diseases both hospitalized in local and non-local medical institutions.Conclusions: All the preliminary results threw light on some defects in the process of medical treatment, which was rationality of choice and direction of diagnosis and treatment. The problem may be caused by included inpatients' incorrect medical concepts, unstandardized diagnosis and treatment behaviours, imperfect medical insurance reimbursement policy, and no adequate capacity to treat difficult and miscellaneous diseases. Under the background of deepening medical reform, the city municipal government needs to further increase the publicity of medical reform and make decisions to adapt to the changes in policy environment, for the medical insurance linkage mechanism with hierarchical medical system.