Objective: Autoimmune thyroid disease, including Graves disease (GD) and Hashimoto thyroiditis (HT), is one of the most common endocrine diseases. GD and HT are the main etiologies for hyperthyroidism and hypothyroidism, respectively. This study aimed to provide a metabolomic analysis of GD patients with hyperthyroidism and HT patients with hypothyroidism. Methods: This study investigated serum metabolomics in 43 GD patients with hyperthyroidism, 45 HT patients with hypothyroidism, and 52 age- and sex-matched healthy controls. The metabolomic data were analyzed by performing multivariate statistical analysis. Results: The 186 metabolites including amino acids, bile acids, free fatty acids, and lipids were identified in all participants. Multivariate models indicated systematic differences in the hyperthyroidism, hypothyroidism, and control groups. Compared to healthy controls, the 22 metabolites in the hyperthyroidism group and the 17 metabolites in the hypothyroidism group were significantly changed. Pathway analysis showed that hyperthyroidism had a significant impact on arginine and proline metabolism and aminoacyl-transfer ribonucleic acid biosynthesis, while hypothyroidism had a significant impact on alanine, aspartate, and glutamate metabolism. Conclusion: The serum metabolomic pattern changes in patients with autoimmune thyroid dysfunction. Abbreviations: BMI = body mass index; CA = cholic acid; CDCA = chenodeoxycholic acid; DCA = deoxycholic acid; FBG = fasting plasma glucose; FINS = fasting plasma insulin; FT3 = free triiodothyronine; FT4 = free thyroxine; GD = Graves disease; GDCA = glycodeoxycholic acid; HDL-C = high-density lipoprotein cholesterol; HOMA-IR = homeostasis model assessment of insulin resistance; HT = Hashimoto thyroiditis; LDL-C = low-density lipoprotein cholesterol; PC = phosphatidylcholine; PCA = principal component analysis; PLS-DA = partial least squares discriminant analysis; SM = sphingomyelin; TBA = total bile acid; TC = total cholesterol; TG = triglyceride; TSH = thyrotropin; VIP = variable influences on projection.