High-quality (HQ) reference genomes are essential for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. However, existing metagenomic binners often fail to reconstruct a reasonable number of reliable HQ genomes owing to a lack of ideal binning guides. Here, we present a single-cell genome-guided binning of metagenomic assemblies (SIGMA) to reconstruct the HQ genomes of multiple strains from microbial communities at once. SIGMA generates self-reference sequences from the same sample by single-cell sequencing and uses them as guides to reconstruct metagenomic bins. The single-cell genome guide enabled precise binning and sequence integration and produced the largest number of HQ genomes from mock community and human microbiota samples in comparison with conventional binners. SIGMA can recover rRNA and tRNA genes and link plasmids to the host. This ability will contribute to understanding intraspecies diversity and distribution of mobile genetic elements in uncultured microbes.