Abnormal liver function (ALF) plays a key role in metabolic syndrome (MetS), but only few data on the relationship between MetS and the risk factors for ALF (e.g., biotoxins) are available. We aimed to provide the prevalence of MetS and its association with the risk factors for ALF in rural area of Southwest China. A cross-sectional study within the hepatocellular carcinoma cohort was conducted, and included 5493 people with age from 30 to 85 years old. MetS was defined according to the Joint Scientific Statement. We observed that the prevalence of MetS was 31.8% (39.0% in women and 19.8% in men). Logistic regression analysis showed that significantly increased risk of MetS was found in those showing ALF (OR = 3.00, 95% CI: 2.43–3.71). Significantly decreased risk of MetS was found in those with higher HBV DNA titers (OR = 0.49, 95% CI: 0.33–0.74), and in those with higher aflatoxin B1 exposure (estimated daily intake, EDI) (OR = 0.60, 95% CI: 0.53–0.67). No significant change was found in those with higher microcystin-LR exposure (EDI). Therefore, the different risk factors for ALF might exert different effects on MetS. However, there should be an interaction effect existing that might decide the severity of MetS.