Perchlorate and chlorate are recognized as ubiquitously inorganic pollutants inenvrionment owing to their high solubility in water and resistance to degradation. Previous studies have confirmed the potential adverse effects of perchlorate and chlorate on human thyroid function, along with implications for fetal growth and development. The fetus grows and develops pregnant women's womb and absorbs nutrients from her body. However, there is still limited information on prenatal exposure to perchlorate and chlorate and the related health risks, especially in China. In this study, a total of 430 serum specimens obtained from pregnant females residing in Southern China were analyzed to ascertain the levels of perchlorate and chlorate, and explore the relationship between perchlorate and chlorate and thyroid function by linear regression, WQS, and QGC. The measured serum levels of perchlorate and chlorate were comparatively elevated, demonstrating median values of 0.693 μg/L and 1.36 μg/L, respectively. The estimated exposure dose of perchlorate in 19.7% of pregnant women exceeded the USEPA reference dose, indicating potential health risks. Although no significant association was found between serum perchlorate and thyroid hormone levels, the exposure to perchlorate for pregnant women in Southern China is cause for concern given their sensitivity to chemicals during pregnancy and the relatively high internal exposure levels.