Vegetation restoration is an effective strategy to improve the ecosystem function of the Loess Plateau. Soil microbiomes play a critical role in maintaining soil multifunctionality (SMF). However, the role of aggregate-scale microbial communities and interactions in regulating SMF during vegetation restoration remains poorly understood. Here, we selected six types of vegetation restoration measures in the Loess Plateau, including natural grassland (NL), Medicago sativa (MS), Hippophae rhamnoides (HR), Caragana korshinskii (CK), Armeniaca vulgaris (AV), and Populus alba (PA), and used abandoned land (AL) as a control to identify key microbial mechanisms driving SMF at the aggregate scale. The results show that vegetation restoration increased bacterial diversity, fungal network complexity, and SMF, especially in AV. In contrast, fungal diversity and bacterial network complexity exhibited asynchronous dynamics across different-sized aggregates. Soil microbial diversity peaked at micro-aggregates (0.053-0.25 mm), while fungal network complexity increased with decreasing aggregate size. The structural equation model confirmed that fungal community composition in large macro-aggregates (>2 mm) and fungal network complexity in <2 mm aggregates were the key drivers of SMF. Our results emphasize the divergent mechanisms by which microbial properties influence SMF across aggregate sizes, highlighting the importance of fungal communities in maintaining soil ecosystem functions.