In the context of increasing grain demand and the urgent need to reduce environmental burdens, sustainable nitrogen (N) management practices are essential for ensuring food security while minimizing negative environmental impacts. This study aimed to exploring a site-balanced N application rate and to determine the impact and primary contributors of optimal N application rate on the N and carbon footprints in the hybrid maize seed production system. A consecutive field experiment of four nitrogen application rates (0, 168, 240, and 320 kg N ha− 1) was conducted. An empirical model was used to assess the reactive nitrogen losses and the life cycle assessment was employed to evaluate the greenhouse gas (GHG) emissions. The grain yield exhibited an increase with the rising nitrogen gradient, peaking at 6.9 Mg ha− 1 under the N240 treatment. Beyond this point, no further yield benefits were observed. Optimal nitrogen rate at N240 significantly reduced reactive nitrogen losses by 24%, and obtained site-specific N balanced status. The average nitrogen footprint of the N240 treatment was 8.1 kg N per Mg, which was significantly 10% lower compared to the N320 treatment. The N240 system exhibited GHG emissions of 5783 kg CO2 eq ha− 1, with nitrogen fertilizer and electricity for irrigation contributing 42–57% and 34–45% of total emissions, respectively. Optimal nitrogen rate achieving higher yields, while obtaining a minimal nitrogen and carbon footprint. Employing appropriate nitrogen rate enhanced the nitrogen absorption by aboveground biomass and grains of hybrid maize seed, thereby reducing nitrogen surplus in soil. This study provides valuable insights for sustainable nitrogen management and carbon footprint reduction strategies in global hybrid maize seed production systems.