Studies have shown that per- and polyfluoroalkyl substances (PFAS) may impact thyroid function in human health. While the consistency between PFAS exposure and thyroid health effects in pregnant women has been validated, the effects on men and non-pregnant women remains inconclusive. To address this, a meta-analysis was carried out in this paper, with 14 eligible studies retrieved from Embase, PubMed, and Web of Science that were published up to 2 June 2024, focusing on the relationship between PFAS exposure and its effect on thyroid hormone levels in the human body. The thyroid function indexes analyzed included thyroid stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), free T3 (FT3), and free T4 (FT4). The estimated value (β) and the corresponding confidence interval (95% CI) were extracted from the literature. A heterogeneity test was carried out, and the sensitivity analysis and publication bias of the studies were analyzed using Stata 18.0. The results revealed that in men and non-pregnant women, PFOA was positively correlated with FT3 (β = 0.011, 95% CI = 0.001, 0.02, I² = 13.4). However, no significant associations were found between exposure to other PFAS and thyroid hormones. A subgroup analysis further indicated that the correlations between PFAS exposure and thyroid hormone levels were more significant in adolescents, in both America and Europe.