Increasing nitrogen (N) and phosphorus (P) input is one of the major contributors to anthropogenic climate change, which can regulate the sequestration and storage of soil organic carbon (SOC) by changing microbial communities and their residues, the significant component of stable SOC. However, it remains unclear how N and P fertilization influence aggregate-associated microbial communities and their residues in P-deficient soils. Answering this question is of great significance to reaching a better understanding of soil carbon cycles under carbon neutrality.