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Background Autoimmune thyroiditis (AIT) frequently coexists with other autoimmune diseases, suggesting shared pathophysiological pathways. However, large-scale evidence supporting the relationship between AIT and rheumatoid arthritis (RA), as well as the potential metabolic and endocrine mediators linking the two, remains limited. Methods A cross-sectional analysis was conducted using nationally representative data from NHANES 2007–2012 (n = 5,715). Multivariable logistic regression models were used to evaluate associations between AIT and RA. Mediation analyses assessed the potential indirect effects of uric acid and free triiodothyronine (FT3). A cross-sectional risk stratification nomogram for RA status among individuals with AIT was constructed. Model performance was assessed in NHANES and examined for consistency in an independent hospital-based clinical cohort from China (n = 196). Results AIT was significantly associated with prevalent RA in the NHANES cohort after multivariable adjustment. Uric acid and FT3 were statistically associated with both AIT and RA in regression analyses. Exploratory mediation analyses suggested that uric acid accounted for a modest proportion of the observed association in NHANES (13.4%), with directionally consistent findings in the external clinical cohort, whereas FT3 demonstrated inconsistent and non-significant mediation across cohorts. The risk stratification model showed good discriminative performance in NHANES (AUC = 0.776) and maintained comparable discrimination in the external cohort (AUC = 0.724), with acceptable calibration. Conclusions In this cross-sectional study, AIT was associated with prevalent RA, and selected metabolic and endocrine biomarkers were statistically related to this association. Although causal inference is precluded by the study design, these findings suggest the presence of shared metabolic and endocrine contexts underlying thyroid and joint autoimmunity and support further longitudinal investigation.