Anthropogenic activities are supposed to reduce global biodiversity and negatively influence the development of diverse groups in the tree of life. Yet how agricultural management shapes the diversity of microscopic organisms and their evolution in the soil, especially at large spatial scale, remains unknown. Here, we investigated how agricultural land-use affected the biodiversity and the underlying evolutionary events of soil nematodes by comparing their communities in natural and agricultural soils covering a latitudinal transect spanning 2500 km across China. In natural habitats, nematode phylogenetic and taxonomic diversity and species richness showed a hump-shaped relationship with latitudes and peaked at 30° N, while in agricultural habitats those community matrices did not change across the studied latitudinal spectrum. Meanwhile, agricultural management reduced both diversity and richness of nematodes with the effect being more pronounced in subtropical zones. However, evolutionary diversification rates were greater in agricultural than in natural habitats across the entire latitudinal range. This was associated with reductions of soil organic carbon and nitrogen as well as shifts of nematode community compositions towards rapidly evolving taxa (r–strategists) in agricultural habitats. Together, our results suggest that the relatively unfavorable environmental status induced by agricultural management could accelerate the community-level speciation rates of nematodes through enriching rapidly evolving taxon. These insights increase our understanding of the systematic impacts of agricultural activities on soil biodiversity that might facilitate conservation and restoration policies for the purpose of sustainable agriculture.