AbstractSoil erosion has become a serious ecological problem hindering the agricultural and economic development in Northeast China. Soil aggregates are basic units that regulate soil fertility and microbial activity. However, there have been few reports on the role of soil erosion in regulating the microbial diversity, multiple ecosystem services, and functions (multifunctionality) of soil aggregates. In this study, we investigated the effects of soil erosion on microbial diversity and the activities of various extracellular enzymes associated with soil aggregates by using Mollisol soil in Northeastern China at different positions of a slope, and how soil erosion affects soil multifunctionality indexes obtained by normalized calculation of soil enzyme activities. The results showed that soil erosion could reduce the physicochemical properties, soil enzyme activity, and microbial diversity of the aggregates, resulting in accumulation of aggregate nutrients and increase in microbial diversity and enzyme activity in the sedimentation area. Compared with smaller soil aggregates, larger soil aggregates had higher nutrient content, enzyme activity, and microbial diversity. However, with the intensification of soil erosion, the differences in microbial diversity and soil enzyme activities among different sizes of aggregates were reduced. Soil erosion also significantly reduced soil multifunctionality (p < 0.001). The multifunctionality of 2000–250 μm, 250–53 μm, and <53 μm aggregates respectively declined from 0.52, 0.20, and 0.08 (no erosion sites) to −0.17, −0.66, and −0.77 (heavy erosion sites). Additionally, microbial diversity was found to have a linear positive correlation with soil multifunctionality (R2 = 0.23, p < 0.01). Structural equation modeling and random forest analysis revealed that soil organic carbon and aggregate water stability are main predictors of soil multifunctionality. Furthermore, soil physicochemical properties had a greater influence on soil multifunctionality than microbial diversity. Collectively, our results demonstrate that soil erosion negatively affects the structure, resource effectiveness, and microbial activity of soil aggregates, thereby reducing to differential soil multifunctionality.