We aim to evaluate the overall survival and associated risk factors for HIV-infected Chinese patients on antiretroviral therapy (ART). 2517 patients receiving ART between 2006 and 2016 were prospectively enrolled in Yunnan province. Kaplan-Meier analyses and Cox proportional hazard regression analyses were performed. 216/2517 patients died during a median 17.5 (interquartile range [IQR] 6.8-33.2) months of follow-up. 82/216 occurred within 6 months of starting ART. Adjusted hazard ratios were10.69 (95%CI 2.38-48.02, p = 0.002) for old age, 1.94 (95%CI 1.40-2.69, p < 0.0001) for advanced WHO stage, and 0.42 (95%CI 0.27-0.63, p < 0.0001) for heterosexual transmission compared to injecting drug users. Surprisingly, adjusted hazard ratios comparing low CD4 counts group (<50 cells/µl) with high CD4 counts group (≥500 cells/µl) within six months after starting ART was 20.17 (95%CI 4.62-87.95, p < 0.0001) and it declined to 3.57 (95%CI 1.10-11.58, p = 0.034) afterwards. Age, WHO stage, transmission route are significantly independent risk factors for ART treated HIV patients. Importantly, baseline CD4 counts is strongly inversely associated with survival in the first six months; whereas it becomes a weak prognostic factor after six months of starting ART.