Excessive nitrogen (N) application in wheat–maize cropping systems was adjusted towards more sustainable practices to reduce hydrological N losses while maintaining crop yield. In comprehensive quantification of N management effects on crop yield, N use efficiency (NUE), hydrological N losses, and soil nitrate residual across eight seasons, we have added to growing evidence of strategies beneficial for sustainable crop production with lower hydrological N losses. The results show that adjusted N practices enhanced crop yield and NUE, as compared to farmer’s practices, but benefits varied with N rates and types. Optimized N treatment (OPT, 180 kg N ha-1 in both maize and wheat seasons) with or without straw returning produced the most crop yield. They increased maize yield by 5.5% and 7.3% and wheat yield by 6.2% and 3.2% on average, as compared to farmer’s practice with huge N application (FP, 345 kg N ha−1 and 240 kg N ha−1 in maize and wheat). Regulation of N release through amendment with controlled release urea at a rate of 144 kg N ha−1 crop−1 (CRU treatment) obtained 4.4% greater maize yield than FP, and sustained a similar wheat yield with less N input, resulting in the highest crop NUE. Additionally, CRU was most effective in mitigating hydrological N loss, with 39.5% and 45.5% less leachate N and 31.9% and 35.9% less runoff N loss than FP in maize and wheat seasons. Synthetic N input correlated significantly and positively with runoff and leachate N losses, indicating it was one of the dominant factors driving hydrological N losses. Moreover, compared to OPT, additional straw returning (STR) or substituting 20% of the nutrients by duck manure (DMS) further reduced runoff N discharges due to the fact that organic matter incorporation increased resilience to rainfall. N over-application in FP caused considerable nitrate accumulation in the 0–90-cm soil profile, while the adjusted N practices, i.e., OPT, STR, CRU, and DMS treatments effectively controlled it to a range of 79.6–92.9 kg N ha−1. This study suggests that efforts using optimized N treatment integrated with CRU or straw returning should be encouraged for sustainable crop production in this region.