BackgroundCaries in young children has received more and more attention. The study of the oral microbiota may help to understand the polymicrobial etiology of dental caries.ObjectivesTo investigate the diversity and structure of microbial communities in saliva samples from 5-year-old children with versus without dental caries.MethodsA total of 36 saliva samples were collected from 18 children with high caries (HB group) and from 18 children without caries (NB group). Then, 16S rDNA was amplified from bacterial samples using polymerase chain reaction, and high-throughput sequencing was performed using Illumina Novaseq platforms.ResultsSequences were clustered into operational taxonomic units (OTUs), which were distributed among 16 phyla, 26 classes, 56 orders, 93 families, 173 genera, and 218 species.Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria,Patescibacteria, Epsilonbacteraeota, Cyanobacteria, AcidobacteriaandSpirochaeteswere basically the same in different groups, but their relative abundances were different. The core microbiome was defined as the species from 218 shared microbial taxa. The alpha diversity test showed that there were no significant differences in microbial abundance and diversity between the high caries and no caries groups. The results from principal coordinate analysis (PCoA) and hierarchical clustering showed that the two groups had similar microorganisms. The biomarkers of different groups were defined by LEfSe analysis to identify potential caries-related and health-related bacteria. Co-occurrence network analysis of dominant genera showed that oral microbial communities in the no caries group were more complex and aggregated than those in the high caries group. Finally, the PICRUSt algorithm was used to predict the function of the microbial communities from saliva samples. The obtained results showed that mineral absorption was greater in the no caries group than in the high caries group. BugBase was used to determine phenotypes present in microbial community samples. The obtained results showed thatStreptococcuswas greater in the high caries group than in the no caries group.ConclusionFindings of this study provide a comprehensive understanding of the microbiological etiology of dental caries in 5-year-old children and are expected to provide new methods for its prevention and treatment.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12903-023-03055-2.