In this work, we investigated exposure levels, distribution patterns, and potential harmful impacts of polybrominated diphenyl ethers (PBDEs) on thyroid hormone activity in 26 children with congenital hypothyroidism and their mothers' pair and 12 normal control pairs. The average concentration of PBDEs in congenital hypothyroidism (median: 22.16 ng/g lipid) was higher than in normal controls (median: 14.76 ng/g lipid), but there was no statistical difference between the two groups. The BDE congeners were dominated by penta- to hepta-BDEs, but the greater brominated congeners (e.g., BDE 197, 196, 207, and 208) were relatively abundant in congenital hypothyroidism. BDE 138 was only observed in the congenital hypothyroidism cases. The maternal transfer and transport ratio of individual BDE congeners was shown for BDE 28 (0.588, p < 0.001), BDE 47 (0.564, p < 0.001), BDE 49 (0.712, p < 0.001) and BDE 119 (0.477, p = 0.002). The thyroid hormones were most obviously influenced by the internal exposure to PBDEs in normal mothers, showing a positive relationship with TSH (0.641 with BDE 154; 0.591 with BDE 153) and FT4 (0.584 with BDE 49; 0.572 with BDE 66) and a negative relationship with T3 (-0.577 with BDE 154) in the normal infants group. No significant correlations were observed in the congenital hypothyroidism cases.