Polychlorinated biphenyls (PCBs) and halogen flame retardants (HFRs) are major pollutants in e-waste recycling area. High internal exposure levels of PCBs and HFRs are harmful to human thyroid hormone (TH) equilibrium. To examine their disrupting effects on TH, we conducted a study on children (n = 114) of an e-waste recycling and a control area in South China. Concentrations of PCBs, HFRs, and TH levels were determined in serum samples. TH related proteins and their corresponding gene were also monitored as markers of such disruption. Levels of these chemicals in the exposed group were much greater than those in the control group. Results of the linear regression and generalized additive model indicated the presence of close relationships between the internal exposure levels and the responses of TH related proteins, gene expression. More extensive exposure concentrations of these chemicals led to higher expression of iodothyronine deiodinase I and decreased the concentrations of thyroid-stimulating hormone, expression of TH receptor α, indicating the exertion of discrepant and even contrary influences on equilibrium of TH, and a compensation of these mechanisms may kept the homeostasis of TH. These results for children warrant further investigation on the health risks of PCBs and HFRs exposure in e-waste area.