After deposition on the topsoil, microplastics (MPs) may be vertically migrated to deeper soil layers over time or eventually enter the groundwater system, leading to more widespread environmental and ecological issues. However, the vertical distribution of MPs in natural soils are not yet fully understood. In this study, we collected soil profiles (0–100 cm) from four different land use types on the west bank of Taihu Lake in China to investigate the vertical distribution and weathering characteristics of MPs. The average abundance of soil MPs followed the pattern of paddy field (490 ± 82 items/kg) > dryland (356 ± 55 items/kg) > tea garden (306 ± 32 items/kg) > woodland (171 ± 27 items/kg) in the 0–10 cm layer, and the abundance of MPs decreased linearly with soil depth (r = −0.89, p < 0.01). Compared to tea garden and woodland, MPs in dryland and paddy field have migrated to deeper soil layers (80–100 cm). The carbonyl index of polyethylene and polypropylene MPs increased significantly with soil depth (r = 0.96, p < 0.01), with values of 0.58 ± 0.30 and 0.54 ± 0.33, respectively. The significant negative correlation between MPs size and carbonyl index confirmed that small-sized MPs in deeper soil layers originated from the weathering and fragmentation of MPs in topsoil. The results of structural equation model showed that roots and soil aggregates may act as filters during the vertical migration of MPs. These findings contribute to a better understanding of the environmental fate of MPs in soil and the assessment of associated ecological risks.