Straw residue amendment and fertilization are the key global management strategies for achieving more sustainable agriculture. However, the temporal changes in labile soil organic carbon (SOC) fractions and microbial community (MB) in response to differential long-term fertilization during straw residue decomposition remain unclear. We collected topsoil samples (0–20 cm; Mollisols) from three fertilizer management strategies (CK, no fertilization control, IF, inorganic fertilizer, and IFM, inorganic fertilizer plus manure) in a long-term field experiment. Subsequently, we conducted an in-situ micro-plot incubation experiment with and without 13C-labeled maize straw residue (δ13C = 246.9‰). We found that the straw-residue C in soil was mainly retained as particulate organic carbon (POC). The residue-derived POC was significantly increased, by 3, 5, and 20 times, whereas the residue-derived dissolved organic carbon (DOC) was significantly decreased by 71 %, 57 %, and 95 % in CK, IF, and IFM treatments, respectively, with straw addition (abbreviated as CKS, IFS, and IFMS respectively) during straw residue decomposition. The content of residue-derived microbial biomass carbon (MBC) was higher at 40.6 mg kg−1 (IFMS) and 33.0 mg kg−1 (IFS) compared to 27.0 mg kg−1 in the unfertilized (CKS) treatment at the end of the incubation period (day 150). The number of edges of the bacterial network was decreased by 16 %, 53 %, and 73 % in the treatments of CKS, IFS, and IFMS, respectively, compared with the corresponding fertilizer treatments without straw application. While the number of edges of fungal network also decreased by 57 % in CKS treatment, those in IFS and IFMS treatments increased by 160 % and 310 %, respectively. This indicated that straw residue addition decreases the bacterial microbial network complexity in all treatments, but it increases fungal network complexity in IFS and IFMS treatments. The highest microbial activities of the bacterial and fungal keystone taxa were observed on the 1 st day in the IFS treatment and on the 150th day in the CKS treatment. However, the highest microbial activities of bacterial keystone taxa were observed on the 60th day, and the highest microbial activities of fungal keystone taxa were detected on the 150th day in the IFMS treatment. The observed temporal changes in the microbial community suggested that independent of agricultural fertilizer management, straw residue-derived POC and DOC promoted fungal C processing, whereas for bacterial C, this was facilitated only by straw residue-derived MBC in these Mollisols. Highlighting straw residue incorporation helps to sustain microbial diversity and associated carbon processing in agricultural soils.