While straw mulching has the potential to reduce fertilizer-nitrogen (N) losses in intensively managed cropland, how soil organic carbon (SOC) regulates this fate of fertilizer-N at soil aggregate or profile scales remains unresolved. Here, micro-plots were nested within a four-year field experiment to assess fertilizer-N fates and their linkages with SOC fractions and stabilization processes via ¹⁵N-tracing and ¹³C natural abundance analyses. Three treatments were included: (ⅰ) conventional N application (FN), (ⅱ) reduced N application (RN), and (ⅲ) reduced N with straw mulching (RS). While RN reduced crop yields compared to FN, RS achieved comparable yields and 7.71% higher N recovery efficiency (P<0.05). The δ¹³C fractionation between aggregates and bulk soil was significantly positively correlated with the fertilizer-N content in the >2 mm and <0.053 mm fractions, indicating that N retention was coupled with SOC stabilization processes. Compared with RN, RS resulted in a 2−3.4 times greater SOC conversion probability into the <0.053 mm fraction and a 1.4 times higher aggregate-associated fertilizer-N content. SOC fractions differentially regulated the profile distribution of fertilizer-N, with nonlabile organic carbon (C) correlated positively, while dissolved organic C correlated negatively but increased plant N recovery. Compared with RN, RS increased the SOC stock by 24%, reduced NO₃⁻-N accumulation by 37%, and immobilized 36% more N into the microbial biomass (P<0.05). Our findings demonstrate that straw mulching increases N recovery by mediating SOC fractionation, stabilization, and microbial N immobilization. These results provide new insights into SOC–N interactions that could aid in the development of optimal soil C and N management strategies.