Diversified crop rotation is crucial for maintaining sustainable agricultural production by improving resource use efficiency, balancing soil nutrients, and preserving biodiversity. Despite these benefits, there is a notable gap in research concerning the nutrient transport characteristics in cash crop-grain rotation systems. This study was to investigate: (i) the nitrogen (N) uptake and distribution among the different plant organs in rotation crops; (ii) the N footprint in different growth seasons in response to crop N fertilization and residual N in the soil; and (iii) the influence of environmental factors on the productivity and N footprint in cash-grain rotation systems. In the three-year rotation system, N fertilizer was applied at the rates of 220, 175, and 130 kg N eq ha−1 for maize, and 300 and 240 kg N eq ha−1 for garlic. Results showed that maintaining a high N application rate during the garlic season and appropriately reducing it during the maize season (G300M175) enhanced N transfer to the grains of maize, increasing maize N use efficiency by 18.9%, while simultaneously increasing garlic dry matter and N accumulation. While the maize yield remained stable, garlic yield decreased with the reduced N rate, resulting in a significant reduction in N footprint. Water supplies (precipitation and irrigation) positively impacted dry matter accumulation, N absorption and yield, while reducing N footprint in both crops. Elevated air temperature favored maize yield but hindered garlic production and raised garlic N footprint. Although N fertilizer increased N footprint per unit land area (NFa), it decreased the N footprint per unit N uptake by crops (NFn) while boosting crop yields. Maintaining a suitable N input rate for cash crops in previous season while reducing N input in the following season staple crops can enhance the whole systems’ productivity while decreasing the nitrogen footprint.
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