As one of the essential components, microorganisms are the cores of biogeochemical circulation in lakes. However, due to the complex interaction among microorganisms and the incomplete description of their habitats, less than 1% of microorganisms in lakes can be cultivated in the laboratory. In the past ten years, metagenomic methods has been widely applied to the microbial researches, which enormously contribute to the understanding of microbiomes in lake ecosystems. The obtained results not only uncovered the composition and diversity of microbial communities, but also revealed the ecological functions of microbes as well as the interactions among microorganisms. Moreover, metagenome-assembled genomes (MAGs) of uncultured microorganisms can be obtained by various contig binning strategies based on metagenomic data mining, which can be subsequently used for comparative genomics and ecological evolution studies. With the continuous development of bioinformatics discipline and the relevant sequencing technologies, metagenomics will become a more powerful tool in basic ecological principle exploration and routine environmental biomonitoring, and also become the cornerstone of understanding the ecosystem function and maintaining the ecological services of lakes.