Background Hydrogen sulfide (H2S) is the most important compound causing oral malodor, and its concentration is thought to be closely correlated with oral microorganism activity. Therefore, clarifying the correlation between oral microbes and metabolites is important. Methods This study tested with 16S rRNA gene amplicon and shotgun metagenomic sequencing of oral microorganisms and oral malodor tests. Results There were different of the microbial taxa between the low and high H2S groups. And in the high H2S group, most of the enriched taxa were genera which abundance was correlated with H2S concentration. Fusobacterium periodonticum and Prevotella nanceiensis were significantly different in coverage breadth and depth and in LPS biosynthesis contributions between the two groups. The contribution of F. periodonticum to sulfur metabolism was significantly different between the two groups, and the relative F. periodonticum abundance was higher in the high H2S group. Conclusions The H2S content is significantly associated with the oral cavity microorganism composition and abundance. Most microorganisms enriched in people with high H2S levels are associated with oral diseases such as caries and periodontal diseases.