Perfluorohexanoic acid (PFHxA) has been recognized as an alternative to the wide usage of perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS) in the fluoropolymer industry for years. PFHxA has been frequently detected in the environment due to its wide application. However, the ecological safety of PFHxA, especially its toxicological effects on aquatic organisms, remains obscure. In the present study, PFHxA at different concentrations (0, 0.48, 2.4, and 12 mg/L) was added to the culture medium for zebrafish embryo/larval exposure at 96 h postfertilization (hpf). Zebrafish larvae showed a slow body growth trend and changes in thyroid hormone levels (THs) upon PFHxA exposure, indicating the interference effect of PFHxA on fish larval development. Moreover, the transcription levels of genes related to the hypothalamic-pituitary-thyroid (HPT) axis were also analyzed. The gene expression level of thyroid hormone receptor β (trβ) was upregulated in a dose-dependent manner. Exposure to 0.48 mg/L PFHxA increased the expression levels of the thyrotrophic-releasing hormone (trh) and thyroid hormone receptor α (trα). Significant increases in corticotrophin-releasing hormone (crh) and transthyretin (ttr) gene expression were also observed when the zebrafish larvae were treated with 12 mg/L PFHxA, except iodothyronine deiodinases (dio1), which decreased obviously at that point. There were significant declines in the transcription of both thyroid-stimulating hormone β (tshβ) and uridinediphosphate-glucuronosyltransferase (ugt1ab) upon exposure to 2.4 mg/L PFHxA. In addition, PFHxA induced a dose-related inhibitory effect on the transcription of sodium/iodide symporter (nis). Finally, the thyroid status will be destroyed after exposure to PFHxA, thus leading to growth impairment in zebrafish larvae.