Indoor dust ingestion is one of the main pathways for human exposure to organophosphate flame retardants (PFRs). The urinary concentrations of diesters (DAPs) are usually used as biomarkers to assess human exposure to PFRs. In this study, the PFR and DAP levels were measured in morning and evening urine samples of 30 workers from an e-waste dismantling site in southern China. The indoor dust samples were also collected from workshops and houses for analyzing associations between PFR and DAP levels in urine and dust. Tris(1-chloro-2-propyl) phosphate (TCIPP) and triphenyl phosphate (TPHP) were the dominant PFRs in dust, while bis(2-chloroethyl) phosphate (BCEP) and diphenyl phosphate (DPHP) were the major DAPs in dust. A significant positive correlation was observed between TPHP and DPHP concentrations in dust (p < 0.001), suggesting their potentially same source and the degradation of TPHP to form DPHP. TCIPP and tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) were the predominant PFRs, and BCEP, bis(1,3-dichloro-2-propyl) phosphate (BDCIPP), and DPHP were the main DAPs in both the morning and evening urine samples. The DPHP levels in evening urine samples were significantly correlated with TPHP and DPHP levels (p < 0.01) in dust. A similar correlation was found for the BCEP levels in the evening urine samples and the TCEP and BCEP levels (p < 0.01) in dust. These results indicated that in addition to being biotransformed from their respective parent PFRs, direct ingestion from indoor dust could also be the potential source for urinary DPHP and BCEP. Since relatively low detection frequencies were observed for bis(1-chloro-2-propyl) phosphate (BCIPP) and bis(butoxyethyl) phosphate (BBOEP) in urine, they may not be the major metabolites of TCIPP and tris(2-butoxyethyl) phosphate (TBOEP), respectively, in the human body. However, BDCIPP can be considered a useful biomarker because it is a unique metabolite of TDCIPP and has high detection frequencies in urine samples. The results of this study indicated the limitations of solely using urinary DAPs as biomarkers for the evaluation of human exposure to PFRs, and certain PFRs as well as hydroxylated PFRs (OH-PFRs) should also be considered for urinary biomonitoring in future studies.