Among many factors affecting dental caries, bacteria are its initiating factor. From the perspective of ecological plaque hypothesis, the application of modern molecular biology methods enable scholars to deeply explore the relationship between the microbial population distribution, biodiversity, microbial community changes of dental plaque biofilm and the occurrence of dental caries in children. The decrease in microflora diversity is closely related to the occurrence of dental caries, which can be detected as early as 6 months before the occurrence of dental caries, providing an important basis for caries monitoring and caries risk assessment. Differential bacteria such as Lactobacillus and Veillonella may be used as biomarkers of caries in children to judge the risk of caries in children. However, current studies have shown that the dominant bacteria in the microbial community structure vary in different processes of caries occurrence and development, that the interaction between different flora is still not clear, and that the specific cariogenic mechanism of the oral plaque microbial community in the process of caries occurrence and development has not been clarified. Further research is still needed to explore the changes in plaque microbial diversity and composition during the development of dental caries and to screen specific dental caries biomarkers. This paper also summarizes the related research findings.