Synthetic nitrogen (N) fertilization is essential for global food security, but often over-applied, causing environmental pollution. Identifying the optimal N application rate that maximizes crop productivity while enhancing key soil properties remains essential for sustainable agriculture. Three treatments from a 21-year field experiment conducted on purple soil in the Sichuan Basin, China, were studied: unfertilized control (CK), moderate synthetic N application (NPK; 130 kg ha(-1)), and higher synthetic N application (HNPK; 170 kg ha(-1)). The results showed that NPK and HNPK increased key soil properties compared to CK, with total N increasing by 44%, microbial biomass N by 48%, microbial biomass C by 81%, and soil organic C by 33% (p < 0.05). Both NPK and HNPK significantly enhanced plant N and C accumulation compared to CK (p < 0.05), resulting in substantial increases in grain yield (436%) and biomass yield (319%). Notably, NPK and HNPK achieved comparable enhancements in soil properties, N use efficiency, and crop productivity (p < 0.05). Additionally, Random Forest model (R-2 = 0.91) identified soil N pools and plant N uptake as primary yield predictors. These findings suggest that moderate N application achieves comparable crop productivity and soil enhancement benefits to higher application rates, supporting resource-efficient agricultural practices that contribute to sustainable intensification in subtropical agroecosystems.