The recurrence rate remains high even under nucleos(t)ide analogues (NUCs) therapy in patients with hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) after resection. The aim of this study is to evaluate the prognostic role of HBsAg in patients undergoing surgical resection for HBV-related HCC in NUCs era. Consecutive 522 patients undergoing surgical resection for HBV-related HCC were retrospectively enrolled. Factors associated with early (within 2 years), late (year 2 to 5), very late (beyond 5 years) recurrence and early or late mortality (within or beyond 5 years) were evaluated. During a median follow-up period of 59 months, 308 (59%), and 146 (28%) patients developed recurrence and mortality, respectively. HBsAg level did not correlate with early recurrence and mortality. By multivariate analyses, HBsAg >200 IU/mL (hazard ratio (HR)=1.778, P=0.037) and presence of cirrhosis (HR=2.157, P=0.001) were independent predictors of late recurrence, while HBsAg >50 IU/mL (HR=4.658, P=0.038), body mass index >25 kg/m (HR=2.720, P=0.013) and significant hepatic fibrosis (HR=2.509, P=0.039) were independent predictors of very late recurrence. HBsAg >50 IU/mL (HR=11.427, P=0.017), age >60 years (HR=2.688, P=0.006), albumin ≤3.5 g/dL (HR=4.739, P<0.001) and presence of cirrhosis (HR=2.781, P=0.006) were independent predictors of late mortality beyond 5 years. Combining these factors could well predict patients with minimal risk of long-term recurrence and mortality. In conclusion, tumor factors, liver function surrogate markers, metabolic factors and serum HBsAg levels play distinct roles in recurrence and survival at different time intervals after surgical resection for HBV-related HCC. Pre-operative HBsAg level is an important predictor of long-term recurrence and survival in patients with HBV-related HCC undergoing surgical resection.