The microorganisms in a healthy child’s oral environment survive in certain proportions and form a stable dynamic balance with the host. If this balance is disrupted, some of the microorganisms become cariogenic microbes and cause early childhood caries (ECC). The changes of cariogenic microbes in this process could be used as biomarkers to assess the caries risk of children and forecast the development of ECC. The relative indices of Streptococcus mutans and the closely related Candida albicans, Bifidobacterium and Streptococci sanguinis may be used as biomarkers to diagnose the susceptibility of children to caries. The detection rate and detection level of Lactobacillus may provide a reference for judging the rate of ECC development.