Co-infection with hepatitis B (HBV) and C (HCV) is common among people living with HIV (PLHIV). This study investigates the impacts of hepatitis co-infection on antiretroviral therapy (ART) outcomes and hepatotoxicity in PLHIV. The cohort study included 1984 PLHIV. Hepatotoxicity was defined by elevated alanine aminotransferase (ALT) levels. ART outcomes were measured by CD4 cell counts, viral load, and mortality rate in patients. Among 1984 PLHIV, 184 (9.3%) were co-infected with HBV and 198 (10.0%) with HCV and 54 (2.7%) were co-infected with HBV and HCV. Of these patients, 156 (7.9%) had ALT elevation ≥ grade 1 at baseline. During the course of ART, the mortality rate and its adjusted hazard ratio (AHR) in PLHIV who were co-infected with HCV (2.6/100 person-years [py], AHR = 2.3, 95%CI 1.1-4.7) was higher than for patients with mono-infected HIV, as it was for those with an elevated ALT (4.4/100 py, AHR = 3.8, [1.7-8.2]) at baseline compared to those with normal ALT. After 6-12 months of ART, the incidence of hepatotoxicity among all the patients was 3.7/100 py. The risk of hepatotoxicity was higher in HCV co-infected (18.6/100 py, adjusted odds ratio [AOR] = 12.4, [8.1-18.2]) than HIV mono-infected patients, and for all regimens (nevirapine: 30.0/100 py, 34.2, 7.3-47.9; zidovudine/stavudine: 24.7/100 py, 22.1, 7.1-25.5; efavirenz: 14.5/100 py, 9.4, 3.5-19.2; lopinavir/ritonavir: 40.1/100 py, 52.2, 9.5-88.2) except tenofovir (4.3/100 py, 4.9, 0.8-9.5). Patients with HBV/HCV co-infected had high hepatotoxicity (10.0/100 py, 6.3, 1.2-23.3) over the same period. Patients with HCV co-infection and HBV/HCV co-infection demonstrated higher hepatotoxicity rate compared with HIV mono-infected patients in China.