Revealing the regional distribution and diversity of fungal sub-communities under different land management practices is essential to conserve biodiversity and predict microbial change trends. In this study, a total of 19 tilled and 25 untilled soil samples across different land-use types were collected from subtropical China to investigate the differences between the spatial distribution patterns, diversity, and community assembly of fungal sub-communities using high-throughput sequencing technology. Our results found that anthropogenic disturbances significantly reduced the diversity of abundant taxa but significantly increased the diversity of rare taxa, suggesting that the small-scale intensive management of land by individual farmers is beneficial for fungal diversity, especially for the conservation of rare taxa. Abundant, intermediate, and rare fungal sub-communities were significantly different in tilled and untilled soils. Anthropogenic disturbances both enhanced the homogenization of fungal communities and decreased the spatial-distance–decay relationship of fungal sub-communities in tilled soils. Based on the null model approach, the changes in the assembly processes of the fungal sub-communities in tilled soils were found to shift consistently to stochastic processes, possibly as a result of the significant changes in the diversity of those fungal sub-communities and associated ecological niches in different land-use types. Our results provide support for the theoretical contention that fungal sub-communities are changed by different land management practices and open the way to the possibility of predicting those changes.