Environmental pollutants have been known to increase the risks of not only respiratory and cardiovascular disease but also metabolic diseases such as obesity and diabetes mellitus (DM). Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) such as benzene and toluene are major constituents of environmental pollution. In the present study, we employed the population of the Korean National Environmental Health Survey (KoNEHS) Cycle 3 conducted between 2015 and 2017, and assessed the associations of urinary biomarkers for PAHs and VOCs exposure with obesity and DM. A total of 3787 adult participants were included and the urinary concentrations of four PAH metabolites and two VOC metabolites were measured. For correcting urine dilution, a covariate-adjusted standardization method was used. The highest quartiles of urinary 2-hydroxynaphthalene (2-NAP) [OR (95% confidence interval (CI)) = 1.46 (1.13, 1.87)] and sum of PAH metabolites [OR (95% CI) = 1.45 (1.13, 1.87)] concentrations were associated with a higher risk of obesity [body mass index (BMI)≥25 kg/m2]. BMI was positively associated with urinary 2-NAP [β (95% CI) = 0.25 (0.09, 0.41), p = 0.003] and sum of PAH metabolites [β (95% CI) = 0.29 (0.08, 0.49), p = 0.006] concentrations. The risk of DM was increased with increasing quartile of 2-hydroxyfluorene (2-OHFlu) and trans, trans-muconic acid (t,t-MA) (p for trend<0.05 and < 0.001, respectively). The highest quartile of t,t-MA showed a significantly higher risk of DM [OR (95% CI) = 2.77 (1.74, 4.42)] and obesity [OR (95% CI) = 1.42 (1.06, 1.90)]. Urinary t,t,-MA level was positively associated with BMI [(β (95% CI) = 0.51 (0.31, 0.71), p < 0.001] and non-alcoholic fatty liver disease index [(β (95% CI) = 0.09 (0.06, 0.12), p < 0.001]. In conclusion, the benzene metabolites t,t-MA and PAH metabolite 2-OHFlu were associated with an increased risk of DM. Urinary biomarkers for PAHs and VOCs were positively associated with BMI in the Korean adult population. Further studies to validate these observations in other populations are warranted.