Purpose Hashimoto's thyroiditis (HT) is a significant public health concern, particularly among females. While existing studies have explored the correlation between serum iron levels and HT, limited research has specifically focused on this association in reproductive-age females. Our study aims to investigate the relationship between serum iron and HT.Methods Using data from the National Health and Nutrition Examination Survey (NHANES) database (2007-2012), we employed weighted multivariate logistic regression models, an XGBoost model, and smooth curve fitting. We assessed the correlation between serum iron and HT and examined linear and non-linear relationships with thyroid peroxidase antibodies (TPOAb) and thyroglobulin antibodies (TgAb).Results Among 2,356 participants, each unit increase in serum iron was associated with a 43% reduced risk of HT (Odds Ratios (OR) 0.574; 95% Confidence Interval (CI) 0.572, 0.576). Quartile analysis confirmed these effects. The XGBoost model identified serum iron as the most significant variable correlated with HT. Smooth curves revealed a linear association between log2-transformed serum iron and HT. Additionally, log2-transformed serum iron inversely correlated with TPOAb levels (beta -15.47; 95% CI -25.01, -5.92), while a non-linear relationship was observed with TgAb.Conclusion Our study reveals that in reproductive-age women, every unit increase in serum iron is associated with a 43% lower risk of HT, demonstrating an inverse relationship. Additionally, serum iron exhibits a negative correlation with TPOAb and a non-linear association with TgAb.