Objective To systematically review the diseases constitution of children in Chinese medical institutions from 2010 to 2016, and to provide evidence for establishing essential medicine list for children (EMLc) of China. Methods We searched PubMed, EMbase, The Cochrane Library, CBM, CNKI, VIP and WanFang Data from January 2010 to February 2016 to collect studies about diseases constitution of Chinese children. Two reviewers independently screened literature, extracted data, and assessed the risk bias of included studies, then data was descriptively analyzed. Results A total of 33 studies of diseases constitution were included, involving 1 797 696 children among 0 to 18 years from 17 provinces of China. Neonatal hyperbilirubinemia, neonatal pneumonia and premature were the main diseases of inpatient newborns. The main diseases of children hospitalized were pneumonia, upper respiratory tract infection and tumor. Upper respiratory tract infection, bronchopneumonia, bronchitis and diarrhea were the main diseases of outpatients. Hyperspasmia, upper respiratory tract infection and pneumonia were the main diseases of emergency patients. Diseases constitution of different medical institution: the main diseases were pathological jaundice, neonatal asphyxia and neonatal pneumonia in both tertiary and secondary medical institution in the newborn group. In the children group, the main diseases were pneumonia, upper respiratory tract infection and bronchitis in both tertiary and secondary medical institution. Besides these diseases, indigestion and fever of unknown origin were also the main diseases of primary medical institution. Disease constitution of different areas: in the newborn group, pathological jaundice, neonatal pneumonia and neonatal hyperbilirubinemia were the main diseases in coastal areas. Neonatal pneumonia, neonatal hyperbilirubinemia and premature were the main diseases in inland areas. Neonatal hyperbilirubinemia, neonatal pneumonia and neonatal hypoxic-ischemic encephalopathy were the main diseases in remote areas. In children group, pneumonia, bronchitis and premature were the main diseases in coastal areas. Pneumonia, bronchitis and hand-foot-and-mouth disease were the main diseases in inland areas. Upper respiratory tract infection, bronchopneumonia and bronchitis were the main diseases in remote areas. Conclusion Diseases constitutions of children vary in different medical institution, and because of extreme lack of date from primary medical institution, we suggest to carry out investigation in primary medical institution to provide evidence for EMLc. Diseases constitutions of children vary in different area, additions should be made according to local conditions when essential drugs of children selected. Newborn, as a special group of children, should be considered separately when EMLc of China established.