Objective: It has been well known that Vitamin D plays an ameliorative effect on the treatment of Hashimoto's thyroiditis (HT), but the underlying mechanism is largely unknown. This study was conducted to analyze the gene network mechanism in the treatment of HT by Vitamin D. Methods: The related genes were retrieved from the GeneCards database using the keywords ‘Hashimoto's thyroiditis’ and ‘Vitamin D’, and the retrieved genes were used to make a Venn intersection map. The obtained genes were used to construct a protein-protein interaction (PPI) network with the STRING database. These key genes were enriched and analyzed by gene ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Results: 602 genes were found to be intersected between HT and Vitamin D. The GO enrichment analysis of HT and Vitamin D is mainly involved in the regulation of T cell activation, leukocyte proliferation, mononuclear cell proliferation, regulation of cell-cell adhesion, lymphocyte proliferation, etc. The results from KEGG pathway analysis were mainly related to Cytokine-cytokine receptor interaction, AGE-RAGE signaling pathway in diabetic complications, Inflammatory bowel disease, Lipid and atherosclerosis, Rheumatoid arthritis, JAK-STAT signaling pathway, EGFR tyrosine kinase inhibitor resistance, human T-cell leukemia virus 1 infection, type I diabetes mellitus, signaling pathway, etc. The top 10 genes of the protein-protein interaction (PPI) network were AGER: S100B, AGO2: DICER1, AGRN: MUSK, AGT: REN, AKT1: NOS3, AKT1: MTOR, ANGPT1: TEK, ANGPT2: TEK, AR: FOXA1, AR: NCOA4. Conclusions: From the analytic results, vitamin D has a regulatory effect on HT.