The correlation between hepatitis B virus (HBV) infection and metabolic syndrome (MetS) remains to be clarified. In this study, we explored this association in a large population in Southwest China. This was a cross-sectional study, with pooled adult health data. Multivariate logistic regression analysis, controlling for age, sex, HBV status, alanine aminotransferase, and fatty liver, was used to identify predictor(s) of MetS. Of the 96,175 participants, positive HBV was identified in 7984 (8.30%) and MetS in 12,092 (12.57%). The MetS prevalence was lower among HBV positive than negative individuals (11.64% versus 12.66%, P < 0.001). The adjusted odds (aOR) of positive HBV among individuals with MetS was 0.841 (95% confidence interval (CI), 0.771-0.916) in men and 0.834 (95% CI, 0.672-0.925) in women. Elevated triglyceride level, a component of MetS, was inversely associated with HBV status in both men and women: aOR, 0.551 (95% CI, 0.514-0.590) and 0.683 (95% CI, 0.605-0.769), respectively. Among HBV positive individuals, liver cirrhosis was more common among those with than without MetS (4.83% versus 2.93%, respectively; P = 0.002). HBsAg-seropositive are inversely associated with MetS, especially elevated triglycerides. Liver cirrhosis was more common among HBV infection patients with MetS.