Among 1550 human immunodeficiency virus (HIV)/Hepatitis B virus (HBV) coinfected individuals receiving antiretroviral therapy (ART) over three years in Guangzhou, China, individuals (8.2%) achieved HBsAg loss. HBsAg loss was positively associated with a longer treatment (median 6.57 years) and a lower HBsAg level (median 645.2 COI) at the baseline. However, HBV pre-genomic RNA (pgRNA), a promising viral biomarker for asserting HBV functional cure, was still detected in 43.9% (44/98) of them, implying an active HBV replication in the HBsAg loss individuals. Our observation suggested that HBsAg loss alone could not reliably predict HBV functional cure in HIV/HBV coinfection.