The role of micronutrients in autoimmune thyroiditis (AIT) has been controversial and lacks sufficient genetic evidence. This study aimed to assess the relationships between various micronutrients and AIT by Mendelian randomization (MR). The single nucleotide polymorphisms (SNPs) of micronutrients and AIT were acquired from IEU Open GWAS project and FinnGen, and were screened according to the basic assumptions of MR. Subsequently, inverse variance weighted was set as the primary tool for MR analysis, with weighted median, simple mode, MR-Egger, and weighted mode set as secondary tools. Next, the MR-Egger intercept was used to assess the horizontal pleiotropy of results. Finally, Cochran's Q test and sensitivity analysis were used to assess the heterogeneity and robustness of the results, respectively. MR analysis showed that vitamin B12 reduced genetic susceptibility to AIT by 83.6% (odds ratio 0.164, 95% confidence interval 0.030 to 0.910, p = 0.039), whereas magnesium, calcium, carotene, copper, folate, iron, potassium, selenium, zinc, vitamin A, vitamin B6, vitamin C, vitamin D, and vitamin E were not associated with genetic susceptibility to AIT (p ≥ 0.05). The MR-Egger intercept showed that these results had no horizontal pleiotropy (p ≥ 0.05). Cochran's Q test and sensitivity analysis showed that these results were not heterogeneous (p ≥ 0.05) and were robust. This study demonstrated that vitamin B12 reduced the risk of AIT, whereas other micronutrients were not associated with the risk of AIT. It provides a new genetic perspective on the pathogenesis of AIT and strengthens the evidence for vitamin B12 as a potential treatment for AIT.