The soil nitrogen (N) and phosphorus (P) availability often constrains soil carbon (C) pool, and elevated N deposition could further intensify soil P limitation, which may affect soil C cycling in these N-rich and P-poor ecosystems. Soil microbial residues may not only affect soil organic carbon (SOC) pool but also impact SOC stability through soil aggregation. However, how soil nutrient availability and aggregate fractions affect microbial residues and the microbial residue contribution to SOC is still not well understood. We took advantage of a 10-year field fertilization experiment to investigate the effects of nutrient additions, soil aggregate fractions, and their interactions on the concentrations of soil microbial residues and their contribution to SOC accumulation in a tropical coastal forest. We found that continuous P addition greatly decreased the concentrations of microbial residues and their contribution to SOC, whereas N addition had no significant effect. The P-stimulated decreases in microbial residues and their contribution to SOC were presumably due to enhanced recycling of microbial residues via increased activity of residue-decomposing enzymes. The interactive effects between soil aggregate fraction and nutrient addition were not significant, suggesting a weak role of physical protection by soil aggregates in mediating microbial responses to altered soil nutrient availability. Our data suggest that the mechanisms driving microbial residue responses to increased N and P availability might be different, and the P-induced decrease in the contribution of microbial residues might be unfavorable for the stability of SOC in N-rich and P-poor tropical forests. Such information is critical for understanding the role of tropical forests in the global carbon cycle.