Abstract: Amino acids, the substrate of protein synthesis, are an important source of energy and nutrition, second only to glucose. Previous studies have found that both microorganisms and their host cells can metabolize amino acids, and the metabolites are widely involved in the regulation of various biological processes, including inflammation and immune response. Exploring the changes in amino acid metabolism during the pathogenesis and progression of diseases has become a new hot topic of research. We summarized in this review the research progress in the pathogenesis and progression of common oral diseases, including dental caries, periodontal diseases, Sjögren’s syndrome, and even oral tumors, related to metabolism pathways of amino acids, especially tryptophan and arginine, and their metabolites, attempting to provide a theoretical basis for enhancing understanding of the pathogenic mechanism of the oral diseases, as well as guidance for clinical treatment.