Novel brominated flame retardant (NBFR) and organophosphate ester (OPE) exposure may engender adverse effects on human health. However, present epidemiological information regarding the effects of such exposure is limited and controversial. In this case−control study, 481 serum samples were collected from patients with thyroid cancer (n = 242) and healthy controls (n = 239) in Shandong Province, eastern China. The levels of NBFRs and OPEs, thyroid hormones, and serum lipid parameters were measured in all the participants. Pentabromotoluene, 2,3-dibromopropyl 2,4,6 tribromophenyl ether, decabromodiphenylethane (DBDPE), tris (2-chloroethyl) phosphate (TCEP), and triphenyl phosphate (TPP) were widely detected (detection frequency > 60%) in all the participants. A significantly high risk association was found between exposure of NBFRs and OPEs (namely 1,2,3,4,5-pentabromobenzene, DBDPE, tri-n-propyl phosphate, tri[(2R)-1-chloro-2-propyl] phosphate, tris (1,3-dichloro-2-propyl) phosphate, and tris (2-butoxyethyl) phosphate) and thyroid cancer in both males and females. In the females of the control group, TCEP levels exhibited a significantly positive association with thyroid-stimulating hormone and a negative association with triiodothyronine (T3), free triiodothyronine (FT3), and free thyroxine (FT4) levels. Weighted quantile sum regression evaluated the mixed effects of the compounds on thyroid hormones levels and thyroid cancer. As a result, TPP accounted for the majority of the T3, thyroxine, and FT3 amounts. Our results suggest that NBFR and OPE exposure contributes to alterations in thyroid function, thereby increasing thyroid cancer risk.