Objective To explore the disease spectrum characteristics of hospitalized children having joined new rural cooperative medical system (NCMS) in Jinjiang, in order to provide reference for developing disease prevention and control measures for the children. Methods The disease spectrum of NCMS hospitalized children under 14 years old in Jinjiang from January to December 2013 were analyzed. Results The NCMS hospitalized children's disease attack was related to age and sex. Children in different age stages had different ranks of disease constitution, but respiratory and digestive system diseases always ranked the top 3 in each age group. The top 5 system diseases affecting children's health were respiratory diseases ( 63 . 60%) , digestive diseases ( 11 . 04%) , certain infectious and parasitic diseases (5.41%), certain conditions originated in perinatal period (3.17%), and certain consequences caused by injury, poison-ing and external causes (2.76%);The top 5 system diseases affected 85.99%of the total hospitalized children. Regard-ing to single disease rank, the top 5 diseases were all respiratory system diseases, (unspecified) bronchial pneumonia (22.83%), (unspecified) acute tonsillitis (9.26%), (unspecified) acute upper respiratory tract infection (8.99%), (unspecified) acute bronchitis (8.82%) and unspecified pneumonia (5.38%); The top 5 diseases affected 55.28% of the total hospital-ized children. Conclusion Respiratory disease is the major disease threatening the children's health in Jinjiang. It is suggested that medical and health resources be adjusted rationally, specific effective methods and measures be taken to prevent respiratory diseases, and relevant prevention and control measures be developed based on the disease constitu-tions of children in different age groups.