The Qaidam Basin on the northern Tibetan Plateau represents a terrestrial Mars-analog desert characterized by hyperaridity, low temperatures, intense ultraviolet radiation, and high-salinity soils. To unveil the largely unexplored genomic diversity of microbes and viruses in this extreme environment, we collected 58 soil samples from various landforms and depths for metagenomic sequencing and analysis. We reconstructed 1,773 microbial metagenome-assembled genomes (mMAGs) and 2,060 viral MAGs (vMAGs), the vast majority (>94%) of which represent novel taxa. Among these, 327 mMAGs (completeness >= 90% and contamination <= 5%) and 325 vMAGs (completeness >= 90%) were classified as high-quality genomes. Taxonomic classification revealed that the bacterial, archaeal, and viral phyla with the largest numbers of genomes were Actinomycetota (n = 565), Halobacteriota (n = 111), and Uroviricota (n = 836), respectively. This metagenomic and genomic dataset provides valuable reference data for advancing our understanding of the diversity and function of microbial and viral communities across global desert ecosystems. Furthermore, these data offer astrobiological insights for research on life in Mars-analog extreme environments.