In this study, eight perfluorinated alkyl substances (PFASs) and five thyroid hormones (TSH, FT4, FT3, TGAb, and TMAb) were determined in 202 human serum samples of the general population of Guangdong, Guangxi and Hainan provinces in southern China. Σ8PFASs concentrations ranged from 0.85 to 24.3 ng/mL with a mean value of 4.66 ng/mL. The PFASs composition profiles of human serum samples nearly make no difference at different locations. A significant increase was observed for ∑8PFASs, PFOS, and PFHxS concentrations with age (p < 0.01). Gender-related differences were found; PFOS, PFHxS, PFBS, and PFOA levels were higher in males (p < 0.05), and the mean concentration of ∑8PFASs was 1.5 times greater in males (6.02 ng/mL) than in females (4.15 ng/mL). PFOS and ∑8PFASs were significantly negatively correlated with FT3 and FT4 and positively correlated with TSH while PFPeA and PFHxA were significantly positively correlated with TGAb and TMAb in all the samples. The opposite associations between FT3, TSH and PFOS, PFOA and PFHxS levels in hypothyroidism and hyperthyroidism group indicate that the PFOS, PFOA and PFHxS enhance the negative feedback mechanisms of the thyroid gland.