<p>Microbial necromass, particularly fungal cell residue, is a primary contributor to soil organic carbon (SOC) formation. Long-term fertilization strongly alters microbial life strategies, thereby influencing the contribution of microbial carbon (C) to SOC formation. Fungal necromass utilization strategies by microorganisms and the mechanisms underlying their contribution to SOC accumulation remain unclear, especially in paddy soils. Therefore, a laboratory incubation study was performed in which ¹³C-labelled fungal necromass (FN) was added to paddy soils collected from long-term (34 years) experimental fields. Three treatments were established: unfertilized (Control + FN), mineral fertilizer application (NPK + FN), and mineral fertilizer combined with chicken manure (NPKM + FN). Incubation was then performed under controlled conditions for 210 days. ¹³C incorporation into phospholipid fatty acids (PLFAs) combined with high-throughput sequencing was performed to trace the detailed fungal residue utilization processes within the microbial food web and their contribution to SOC formation. When ¹³C-labelled fungal necromass was added to the soils, 58–70% was lost as CO₂ after 210 days and ¹³C-CO₂ increased by 16–19% in fertilized soil compared to unfertilized soil. This suggests that the available nutrients increased the microbial activity and biomass-C, thereby accelerating the mineralization of fungal residues.¹³C from the fungal necromass was initially incorporated into Gram-positive (Gram⁺) bacteria, follow by saprotrophic fungi. Subsequently, ¹³C was transferred from Gram⁺ bacteria to Gram-negative (Gram⁻) bacteria and actinomycetes. The combination of mineral fertilizers with manure increased the utilization and turnover of fungal residues by Gram⁻ bacterial and fungal <i>r</i>-strategists (<i>Ascomycota</i>), thereby facilitating the incorporation of ¹³C from fungal residues into SOC. The present study highlights the importance of simultaneously applying mineral and organic fertilizers to paddy soils to efficiently utilize microbial residues and accelerate SOC turnover.</p>