There is limited long-term data on the effect of ART on clinical outcomes in HIV/HBV patients in China. The objective of this study was to understand the ART treatment effect and the factors associated with the loss to follow-up or death of HIV/HBV co-infected patients in the city of Beijing, China. Methods: This study examined clinical indicators for HIV mono-infected or HIV/HBV co-infected patients from Jan. 2010 to Sep. 2018. Included patients were followed for a mean duration of 34.5 months after ART. Covariance analysis for repeated measures was used to analyze the changes of clinical indicators; multivariate logistic regression and Cox model were used to analyze the influencing factors of the abnormal incidence of clinical indicators and the lost to follow-up or death in HIV patients. Results: A total of 841 HIV/HBV co-infected patients and 2000 HIV patients were analyzed. Adherence was estimated to be 93% in all patients. At baseline, ALT, AST, OIs and APRI≥0.5 in HIV/HBV patients were higher, while the CD4 and CD4/CD8 ratio were lower. After ART treatment, the rate of APRI≥0.5 (4.4%) were still higher in HIV/HBV patients and HBV co-infection affect the prevalence of APRI≥0.5 (OR=2.745, 95% CI 1.041-7.243). The variables related to LTFU or death in HIV patients were initial CD4 (HR=0.784, 95% CI 0.652-0.943), APRI≥0.5 (HR=4.647, 95% CI 1.331-16.227), OIs (HR=4.910, 95% CI 2.352-10.247) and age (HR=1.336, 95% CI 1.004-1.778). HBV coinfection was not associated with increased LTFU or overall mortality in HIV patients (p>0.05). Conclusion: With good ART treatment and adherence rate, the clinical indicators were improved significantly in HIV/HBV co-infected patients. However, the incidence of hepatic fibrosis was higher in these patients.