Microbial metabolomics began in 1992, and research on this field includes sample collection, sample testing, and data analysis. Early microbial metabolomics is mainly utilized for the biological identification and characterization of different strains. At present, metabolomics has been applied to microbial phenotypic classification, mutant screening, metabolic pathway and metabolic engineering, control and optimization of fermentation engineering and microbial contaminants, and so on. In dentistry, microbial metabolomics technology has been applied in microbial identification, dental caries, periodontal disease and oral cancer, and cleft lip and palate. Analysis of cariogenic bacteria and periodontal pathogen metabolites in the oral cavity is a common practice. Given its accuracy in differentiating different strains, microbial metabolomics technology is expected to become a new technique for the rapid identification of oral microorganisms. This paper reviews the progress in the study of microbial strategies and applications of metabolomics and presents the problems that may be faced in future studies.