Integrated organic-inorganic fertilization offers the potential to mitigate nitrogen (N) losses while enhancing soil biodiversity. However, a critical knowledge gap remains in understanding how soil micro-food webs regulate N dynamics across different crop growth stages and their functional linkages to seasonal N losses. To address this, we assessed four treatments from a 21-year field experiment: unfertilized control (CK), synthetic fertilizers (NPK), and partial substitution of synthetic N with pig slurry (OMNPK) or crop residues (CRNPK). We quantified total N losses via ammonia volatilization, nitrous oxide emission, and nitrate runoff and leaching, evaluated crop performance, and examined the influence of structural changes in soil micro-food webs at the seedling, silking, and harvesting stages of maize on these processes. The results showed that OMNPK exhibited comparable total N losses to NPK (50.9 vs. 48.3 kg N ha-1). Conversely, CRNPK reduced total N losses by 21 % compared to NPK (38.0 vs. 48.3 kg N ha-1) without decreasing grain yield (P < 0.05). Soil micro-food web analysis revealed that CRNPK enhanced the richness of phylum-level topologically important (TI) bacterial taxa (dominated by Bacteroidota) at the seedling stage, with a convergence in richness across treatments during the silking and harvesting stages. Additionally, stage-specific Random Forest models predicting total N losses (R2 = 0.68-0.79) identified TI bacterial taxa as the dominant predictor at the seedling stage, while fungal diversity emerged as a significant predictor during the silking and harvesting stages. These findings demonstrate that integrating crop residues with synthetic fertilizers effectively balances crop productivity and environmental sustainability by reducing total N losses through stage-specific restructuring of the soil micro-food web, providing an improved mechanistic understanding for managing sustainable agroecosystems.