Objective <p>The association between autoimmune thyroiditis (AIT) and breast cancer was still confused and the mediators was not cleared. In this study, we designed to search a probably causality and mediators between AIT and breast cancer.</p> Method <p>We adopted a bidirectional Mendelian Randomization (MR) analysis to explore the causal association and the potential mediating effects. We used Genome-Wide Association Studies (GWAS) data to construct instrumental variables. We extracted single nucleotide polymorphisms (SNPs) which were significantly associated with exposure factors and the significance threshold was set at <i>p</i> &lt; 1.0 × 10 ⁻⁵. Inverse variance weighted (IVW) is adopted as the main method.</p> Results <p>When AIT was exposed, all the methods indicated that AIT increased the risk of breast cancer (OR values were all &gt; 1 and <i>P</i> &lt; 0.05). When breast cancer was exposed, no significant result was found. Single-factor MR analysis was used for 1400 metabolites and 211 gut microbiome, and showed AIT has a significant causal relationship with 7-methylxanthine IVW: (95% CI 0.001–0.059; <i>p</i> = 0.039). In reverse, there was no causality. 7-Methylxanthine has a causal relationship with breast cancer (95% CI 1.032–1.203; <i>p</i> = 0.006). Multi-factor MR analysis was adopted by adding of 7-methylxanthine to AIT on Breast cancer, the result was still significant, the AIT IVW (95% CI 0.007–0.055; <i>p</i> = 0.011), 7-methylxanthine IVW (95% CI 0.031–0.200; <i>P</i> = 0.007).</p> Conclusion <p>AIT can increase the risk of breast cancer, there is no causal link in the reverse direction. Among the 1400 metabolites, 7-methylxanthine is a mediator of AIT to breast cancer. There were no mediators from AIT to breast cancer in the 211 gut microbiome taxa.</p>