Microorganisms are instrumental in the genesis of microbial necromass carbon (MNC). However, the depth-specific microbial regulatory mechanisms (e.g., diversity, life-history strategies, keystone taxa) modulating MNC accumulation across soil profiles under long-term agricultural management with distinct root distributions remain to be explicitly addressed, especially within the ecologically fragile Loess Plateau. To fill this gap, we investigated amino sugars and microbial community characteristics in the topsoil (0-20 cm, widely recognized as an active layer) and subsoil (140-200 cm, representative of the region's stable layer) of three long-term cropping systems with distinct root distribution depths. Our core discovery reveals a clear shift in microbial drivers regulating MNC across the soil profile: MNC accumulation is bacteria-dominated in topsoil but fungi-dominated in subsoil. Specifically, topsoil MNC was primarily regulated by bacterial alpha-diversity, community composition, and bacterial r-strategists (which were negatively correlated with MNC), whereas subsoil MNC was dominated by fungal alpha-diversity and fungal K-strategists. Keystone taxa also exhibited depth-specific effects: bacterial keystone taxa strongly modulated topsoil MNC, while fungal keystone taxa had a more significant correlation with subsoil MNC. Quantitatively, subsoil MNC content ranged from 62.2% to 74.5% lower than that of the topsoil, and its contribution to soil organic carbon ranged from 26.3% to 44.7% lower (p < 0.01). These findings provide actionable insights for sustainable land management on the Loess Plateau: optimizing subsoil fungal community characteristics can enhance MNC accumulation, supporting land degradation mitigation and improved soil carbon sequestration.