Hepatitis E virus (HEV) infection in immunocompromised patients often results in distinct outcome, compared to the infection in general population. This study aimed to investigate the prevalence, potential risk factors, and clinical features of HEV infection among HIV patients treated with antiretroviral therapy (ART) in Yunnan province, China. A total of 770 HIV-infected patients between May 2015 and February 2016 were enrolled in Yunnan, China. All patients received ART. All plasma samples were tested for anti-HEV IgG, anti-HEV IgM antibodies using ELISA kits, and HEV RNA by real-time qRT-PCR. Association between anti-HEV antibody positivity and demographic, clinical and laboratory measures was assessed in univariate and multivariate logistic regression models. Of the 770 HIV-infected patients, 342 patients (44.42%) were anti-HEV IgG antibody positive, and six patients (0.78%) were anti-HEV IgM antibody positive. None of the patients was HEV RNA positive, as tested in our assays. We found that age, gender, CD4 cell count, WHO stage, marital status, and total cholesterol levels were associated with HEV infection. We report a high seroprevalence rate and several potential risk factors of HEV infection in a large HIV cohort from Yunnan province in China. Further research on identification of the circulating HEV strains and the clinical outcome of this patient population is required.