Widespread exposure to organophosphorus flame retardants (OPFRs) has been observed in the general population. Emerging studies have revealed OPFRs possess endocrine-disturbing properties. The present study aims to assess the association between urinary metabolites of OPFRs, BMI, and serum lipid profiles. Data from the National Health and Nutrition Examination Survey (NHANES) 2017–2018 were obtained, with 1334 adults enrolled in the current study. Urinary concentrations of bis (1-chloro-2-propyl) phosphate (BCIPP), bis(2-chloroethyl) phosphate (BCEP), bis(1,3-dichloro-2-propyl) phosphate (BDCPP), dibutyl phosphate (DBUP), and diphenyl phosphate (DPHP) were quantified to assess OPFR exposure. Covariate-adjusted linear and logistic regression models were conducted to explore the associations between log2-transformed concentrations of OPFR metabolites, BMI, obesity, and serum lipid profiles. Stratified analyses were performed to assess the heterogeneity of associations by age, gender, race, etc. Positive associations were found between OPFR exposure and the risk of obesity. The multivariate linear analysis indicated that a one-unit increase in log2-transformed urinary concentrations of BCEP and BDCPP was associated with 0.27 (95% CI: 0.02–0.52, p = 0.0338) and 0.56 (95% CI: 0.25–0.87, p = 0.0004) higher BMI value, respectively. One log2-unit increase in urinary BCEP and BDCPP concentrations was associated with 1.1-fold (95% CI: 1.02–1.18, p = 0.0096) and 1.19-fold (95% CI: 1.09–1.30, p = 0.0001) risk for developing obesity. Furthermore, the non-linear relationship between exposure to OPFRs and obesity was identified. Additionally, multivariable linear regression showed that urinary DPHP concentrations were inversely correlated with serum triglyceride (TG) levels (β = −7.41, 95% CI: −12.13 to −2.68, p = 0.0022). However, no other OPFR metabolites were found to be significantly statistically associated with serum lipid levels after adjusting for potential confounders. In conclusion, environmental exposure to OPFRs might contribute to obesity and dysregulated TG concentrations in adults. Future prospective research is warranted to confirm the causal relationship between metabolites of OPFRs and obesity.