Objectives To investigate the disease composition and medical costs of in patients with chronic kidney disease (CKD) in People's Hospital of Xinjiang Uygur Autonomous Region from 2012 to 2017. Methods To retrieve the records of patients with CKD, and to classify the main diagnosis of the first page of the medical record according to the International Classification of Diseases (ICD-10) standard. Data was analyzed using Excel 2010 and SPSS 19.0 software. Results A total of 11 650 CKD patients were included, with a sex ratio of 1.48 to 1. The patients were mainly young and middle-aged, accounting for 75.56%. The top 11 diseases of CKD patients were chronic glomerulonephritis, membranous nephropathy, diabetic nephropathy, IgA nephropathy, hypertensive nephropathy, minimally pathological nephritis, focal segmental glomerulosclerosis, lupus nephritis, Polycystic kidney disease, chronic interstitial nephritis and purpuric nephritis. The per capita hospitalization days of CKD patients was 11.23 days, and the per capita medical expenses was 1.51 million yuan. Significant differences were found in different genders, ethnic groups, age groups, disease composition and CKD staging. The medical expenses of CKD patients were mainly medicine and inspection fees, accounting for 71.35%. Conclusions Inpatients of CKD in the People's Hospital of Xinjiang Uygur Autonomous Region have a heavy disease burden and large difference in their conditions.