The incidence of metabolic syndrome (MetS), which causes heart disease and stroke, has increased significantly worldwide. Although many studies have revealed the relationship between heavy metals (cadmium, mercury, and lead), the sum of metabolites of di(2-ethylhexyl) phthalate (DEHP), and MetS, the results remain inconsistent. No study has reported the association between various volatile organic compounds (VOCs) and phthalate metabolites with MetS. This cross-sectional study of a representative sample of adult South Koreans aimed to evaluate the relationship between heavy metals, VOC metabolites, phthalate metabolites, bisphenol A and MetS after adjusting for demographic variables. Data from the Korean National Environmental Health Survey II (2012–2014) (n = 5251) were used in the analysis. Multiple logistic regression analysis was performed for MetS with log-transformed hazardous material quartiles after covariate adjustment. Urine muconic acid (MuA) and mono- (2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) levels were significantly associated with MetS after adjusting for confounders (odds ratio: 1.34 and 1.39, respectively). Urine MuA and MEHHP levels were significantly associated with MetS. Because of the rarity of this study, which investigated the relationship between each VOC and phthalate metabolite with MetS and the strict definition of all indirect measures of MetS components, further research is needed.