Metabolomics reflects the endogenous metabolite changes in organisms through qualitative and quantitative detection of small molecules in biological samples, revealing the metabolic changes during disease development. Metabolomic studies of periodontitis further elucidate the etiology, diagnosis and predictive markers of periodontitis at the levels of metabolites and metabolic pathways. In this paper, the concept and research methods of metabonomics were summarized, and the current status of the metabonomics of saliva and gingival crevicular fluid in the study of periodontitis was reviewed. Previous studies have shown that metabolites such as short-chain fatty acids and amino acids and metabolic pathways such as glutamic acid and pyrimidine metabolism might promote the occurrence of periodontitis, and it was suggested that lactic acid, γ-amino-butyrate, butyric acid and lysophosphatidic acid might be potential diagnostic markers of periodontitis. The metabolomics study of periodontitis still faces challenges such as high heterogeneity of results and fluctuation of metabolites. In the future, its study could be optimized through multicenter prospective studies to provide fresh approaches for the etiology and diagnosis of periodontitis.