With the rapid development of molecular biology technology, especially the application of metagenomics, many challenges in groundwater microbial research have been overcome. Metagenomics has enabled the exploration of the diversity of unculturable microorganisms in groundwater. This paper reviews macro genomics 16S rRNA and metagenomics sequencing data, highlighting recent applications of metagenomics in investigating groundwater microbial communities. It also examines the relationship between microbial diversity and environmental factors, the identification of functional microbial groups, the role of microorganisms in groundwater pollution remediation, and their contribution to the hydrogeochemical cycle. Finally, it provide insights into future research directions in groundwater microbiology.