Abstract: The substitution of mineral fertilizers with manure has profound implications for soil nitrogen dynamics, including nitrogen transformation processes, loss pathways, and overall nitrogen balance. This study aimed to evaluate the impact of partial manure substitution on nitrogen loss, soil nutrient status, and crop productivity through a two-year field experiment from 2021 to 2023 at the Luancheng Agro-Ecosystems Experimental Station, Chinese Academy of Sciences. The experiment involved two types of manure fertilizer (cattle and sheep manure) and four substitution ratios (manure replacing 100%/70%, 50%, and 30% of mineral fertilizers, and mineral fertilizer only as control). The effects of different manure substitution ratios were evaluated in terms crop yield, nitrogen loss in various forms, and the nitrogen balance. The results demonstrated that manure substitution significantly reduced gaseous nitrogen losses compared with mineral fertilizer treatment. Especially in the 2023 maize season, the cumulative N₂O emission of all manure substitution of mineral fertilizers treatments was reduced compared with chemical fertilizer alone, with an average reduction of 33.87%. Furthermore, manure substitution treatments reduced nitrogen loss through ammonia volatilization by 14.60%–68.92% throughout the entire crop growth cycle. These reductions in gaseous nitrogen emissions suggested that manure substitution can effectively minimize gaseous nitrogen losses, thereby enhancing nitrogen use efficiency and lowering the environmental footprint of the fertilization practices. In terms of nitrogen leaching, the substitution of mineral fertilizers with manure reduced the soluble nitrate nitrogen leaching at 100 cm (44.17%–72.72%) and 150 cm (56.95%–79.31%) soil layer, and soluble total nitrogen leaching at 100 cm (26.75%–52.60%) and 150 cm (38.48%–70.70%) compared with that in the treatment of mineral fertilizer only. The leaching risk of the substitution of mineral fertilizers with cow manure treatment was lower than that of the substitution with sheep manure treatment. Taking 150 cm as the leaching interface, the soluble nitrate nitrogen and soluble total nitrogen leaching of the substitution of mineral fertilizers with cow manure treatment decreased by 6.39% and 1.71%, respectively, compared with that of the substitution with sheep manure treatment. However, the proportion of soluble organic nitrogen in the leachate increased with increasing manure substitution ratio from 29.35% to 33.82% at 100 cm soil layer and from 25.31% to 36.65% at 150 cm soil layer, indicating a heightened risk of organic nitrogen leaching at higher dose of manure application. In terms of nitrogen supply capacity, under multi-season application of manure as a substitute for mineral fertilizer, the soil nutrient supply capacity and crop nitrogen use efficiency were both improved. This ensured that wheat and maize yields showed no significant difference compared to mineral fertilizer applied only. Among different treatments, 50% sheep manure substitution balanced between minimizing nitrogen loss and sustaining high crop yield most effectively, suggesting its suitability for maximizing both environmental and agronomic benefits. In summary, substituting mineral fertilizer with manure can effectively reduce nitrogen losses by minimizing gaseous nitrogen emissions and leaching, while simultaneously improving soil nutrient availability and crop productivity. Across treatments, 50% sheep manure substitution is the most sustainable and practical option for minimizing environmental risks while maintaining high yield. These findings provide valuable insights for the rational utilization of manure and other agricultural residues in integrated crop-livestock system, particularly in the North China Plain, and support efforts toward sustainable agricultural intensification.