Objective To investigate the association between costs of hospitalized patients with diabetes mellitus and their complications in the West China Hospital of Sichuan University, so as to provide baseline data for further research. Methods We extracted the hospitalization case data of hospitalized patients with diabetes mellitus who were discharged from the department of endocrinology and metabolism, or discharged after being transferred to other departments for treatment from January 2011 to December 2012, using the hospital information system (HIS) of the West China Hospital of Sichuan University. The data included baseline of hospital patients, discharge diagnosis, hospitalization costs, and if their medical insurance had been registered in hospital. Then, we classified the diseases according to ICD-10 based on discharge diagnosis, coped the data using Excel 2010 software, and conducted statistical analysis using SPSS 13.0. Results a) In 2011, acute and chronic diabetes complication in diabetes inpatients were 11.9% (166/1 396) and 67.1% (930/1 396), respectively. Most of them had peripheral neuropathy and peripheral vascular disease. b) The most frequently-occurred complications were hypertension, followed by dyslipidemia, and osteoporosis. c) The median hospital stay was 13 days (7 to 9 days), and the median total cost of hospital/person-time was 6 578.88 yuan (4 186.93 to 10 953.89 yuan). d) The total cost and duration of hospitalization increased along with the increasing number of the chronic complications of diabetes. e) The diabetic foot patients were 255 person-times, the median duration of hospitalization was 18 days (13 to 29 days), and the median total cost of hospital/person-time was 16 672.19 yuan (10 903.93 to 28 530.37 yuan). Diabetes patients with foot complication had higher total costs and longer duration of hospitalization than those without foot complication. Conclusion Diabetes mellitus is one of the most important diseases in the department of endocrinology and metabolism, which is heavy disease burden. The costs of hospitalization and chronic complications are closely associated. Among these complications, diabetic foot is the heaviest disease burden.