Background Microbial necromass is recognized as the primary contributor to soil organic carbon (OC) storage. However, the patterns and driving factors of microbial necromass carbon (MNC) redistribution across soil aggregates following vegetation restoration in karst areas remain poorly understood. Aims and methods This study examined MNC, microbial community, nutrient content, and exchangeable calcium across three soil aggregate fractions: microaggregates (< 0.25 mm, MI), small macroaggregates (0.25-2 mm, SMA), and large macroaggregates (> 2 mm, LMA). Samples were collected from surface soils under different vegetation restoration types (grassland, shrubland, and secondary forest) in a karst rocky desertification area, with cropland serving as the control. Results Vegetation restoration increased MNC, bacterial necromass carbon (BNC) and fungal necromass carbon (FNC) contents in all aggregates size fractions. The contents of MNC, BNC and FNC gradually increased with decreasing soil aggregate sizes. Higher MNC, BNC, and FNC contributions to aggregate associated OC were observed in SMA and LMA. Secondary forest provided the lowest contributions of BNC, FNC, and MNC to aggregate associated OC. The contribution of FNC considerably exceeded that of BNC (32.04% vs. 5.18%, respectively). The FNC/BNC increased with decreasing aggregate size, except in cropland. Nutrient availability primarily influenced MNC accumulation in LMA, and nutrients and microbial properties affected MNC in SMA. In MI, nutrients and exchangeable calcium influenced MNC accumulation Conclusions Vegetation restoration promoted MNC accumulation through aggregate size distribution regulation. Aggregate size variations led to distinct nutrient, mineral, and microbial characteristics, which determined FNC and BNC proportions and facilitated MNC accumulation.