Organic substitution management (OSM) is critical for soil conservation and nitrogen efficiency. However, integrated assessment of soil quality and crop productivity under paddy‐upland rotation systems after OSM introduction is still lacking. Here, soil nitrogen‐related properties and crop nitrogen use efficiency (NUE) were evaluated in 2018, 2019, and 2020, based on a long‐term rice‐fava bean rotation experiment started in 2015. In comparison to chemical fertilization, OSM increased total soil nitrogen (TN) and available nitrogen (AN) by 13.1% and 13.8%, respectively, during the rice season, and by 16.3% and 15.9% during the fava bean season. However, NUE, nitrogen recovery efficiency (NRE), and nitrogen agronomic efficiency (NAE) all showed season‐specific responses to OSM. OSM decreased NUE, NRE, and NAE by 18.2%, 37.5%, and 26.2% in the rice season but increased by 8.0%, 231.0%, and 184.1% in the fava bean season. From the rotation system scale, there were no significant differences in NUE and nitrogen surplus between the treatments. We suggest that the differences in soil conditions and crop requirements between seasons play significant roles in the response of nitrogen accumulation and nitrogen utilization to OSM. Based on these differences, OSM achieves inter‐seasonal synergy in soil N pools and crop uptake, and results in yield stabilization and soil nitrogen accumulation. Because of its high capacity for improving soil quality while ensuring no yield reduction, OSM has the potential to curb regional soil degradation in paddy‐upland rotation areas where there is increasing demand for food and chemical fertilizers are currently abused.