Objective To evaluate the expression of the total serum IgG and IgG subclasses of anti-PDIA3 antibody (PDIA3 Ab) in patients with autoimmune thyroiditis (AIT) and discuss its association with thyroid peroxidase antibody (TPOAb), thyroglobulin antibody (TgAb), and thyroid function. Methods The PDIA3 Ab total serum IgG and IgG subtype levels were detected by ELISA and thyrotrophin (TSH), free triiodothyronine (FT3), free thyroxine (FT4), TPOAb, and TgAb serum levels were detected by electrochemiluminescence immunoassays. Results Levels of PDIA3 Ab total serum IgG, IgG1, and IgG3 in patients in the AIT group were significantly higher than those in the non-AIT group (P ＜ 0.05). There were no significant differences in PDIA3 Ab total IgG and IgG subtype levels in the AIT with euthyroidism group and hypothyroidism group (P＞ 0.05). In the AIT with hypothyroidism group, PDIA3 Ab IgG1 subtype serum level was negatively correlated with that of TgAb (r =-0.679, P ＜ 0.05), and positively correlated with that of TSH while controlling the variables of TPOAb and TgAb (r = 0.550, P ＜ 0.05). No significant correlation was found among PDIA3 Ab total IgG and IgG3 subclass, TPOAb, TgAb, TSH, FT3, and FT4 in AIT (P＞ 0.05). Conclusion Apart from thyroid peroxidase and thyroglobulin, PDIA3 may be a non-classical autoantigen of AIT and may play an important role in thyroid-related injury.