With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.