Globally, the overall mortality rate among HIV-infected patients has significantly declined during the HAART era. Deaths among HIV-infected inpatients need to be characterized in order to formulate intervention strategies to further improve medical care for this population and their prognosis. In the current study, deaths among HIV-infected inpatients from 2006 to 2015 at a medical center for HIV infection and AIDS patient care in Shanghai, China were retrospectively analyzed. Trends in mortality rates and the proportion of deaths caused by AIDS or non-AIDS-related illnesses were evaluated. A bivariate analysis was performed to identify the demographic and clinical factors associated with AIDS or non-AIDS-related deaths among HIV-infected inpatients. Among 6,473 HIV-infected patients who were discharged from 2006 to 2015, 326 deaths (5.04%) were identified. The yearly mortality rate declined significantly over time (χ2 = 34.41, p < 0.001). Results revealed that most deaths were attributed to AIDS-related illnesses (76.9 %, 233/303), and the proportion of causes of death did not change significantly over time (χ2 = 13.847, p = 0.127). Bivariate analysis identified characteristic factors associated with AIDS-related mortality. Compared to patients who died of non-AIDS illnesses, patients who died of AIDS-related illnesses had a CD4+ T cell count lower than 50 cells/μL (OR 4.587, 2.377-8.850) and fewer liver (OR 0.391, 0.177-0.866) or renal comorbidities (OR 0.188, 0.067-0.523) on admission. Results indicated that the overall in-hospital mortality rate among HIV-infected patients has declined over the past decade. However, AIDS-related illnesses were still the major causes of deaths among HIV-infected inpatients, suggesting that further efforts are needed to improve AIDS care in China.