Objectives This study investigated the impact of fertilization technologies on soil nitrogen leaching and greenhouse gas emissions in a wheat–corn rotation system, in order to provide an effective measure to reduce greenhouse gas emissions and nitrogen loss in the wheat–corn rotation system in North China.

Methods A three-year, six season field experiment was conducted in Xinji City, Hebei Province from 2021 to 2023. Of the five treatments, applying 100% amount of recommended fertilizer was control (T), applying 80% of the recommended fertilizer amount (TM), and at the base of recommended amount, replacing 20% of nutrient with bio-organic fertilizer (TM+1), TM+1 combined with 6000 kg/hm² biochar (TM+2), and TM+2 combined with 15 kg/hm² soil conditioner (TM+3). The amount of fertilizer applied in each treatment was the same in corn season. The soil greenhouse gas (N₂O, CH₄, and CO₂) emissions were monitored regularly across the third experimental year of the rotation system, global warming potential was calculated according to the monitoring results. After harvest of corn, 0–400 cm soil profile was sampled at 100 cm interval to measure the nitrate nitrogen content, and wheat and corn yields were recorded every season.

Results The trends in greenhouse gas emission fluxes from the cultivated layer of soil under different fertilization treatments were relatively consistent. Compared to treatment T, the average N₂O emission flux of treatment TM was significantly decreased by 35.31% (P<0.05); there was no significant difference in the average CO₂ emission flux among the TM, TM+1, TM+2, and TM+3 treatments; similarly; there was no significant difference in CH₄ emission fluxes among the treatments (P>0.05). The annual cumulative N₂O emissions in TM treatment were significantly reduced by 37.63% compared to treatment T (P<0.05), with no significant difference in cumulative CO₂ emissions (P>0.05); the cumulative CH₄ emissions in T, TM, TM+1, TM+2, and TM+3 treatments were all negative values. The global warming potential of TM treatment compared to T treatment was significantly reduced by 38.15%, and that of TM+1 treatment was reduced by 16.25% (P<0.05). Soil nitrate nitrogen peaked at 80–160 cm in TM, TM+1, TM+2, and TM+3 treatments, with the cumulative amount of nitrate nitrogen in the 0–100 cm soil layer in TM, TM+1, TM+2, and TM+3 treatments decreased by 38.98%, 26.05%, 61.26%, and 28.13% respectively compared to T treatment, and the cumulative amount of nitrate nitrogen in the 100–400 cm soil layer for TM, TM+2, TM+3 treatments decreased by 59.26%, 18.03%, and 16.65%, respectively, compared to T treatment. Over the three rotation seasons, the yield of TM+1 and TM+2 treatments showed a significant increase of 9.63% and 9.55% respectively compared to T treatment in the third season (P<0.05).

Conclusions Applying 80% of the recommended formula fertilizer, or under the condition that the total amount of nutrients is not reduced, replacing 20% of the chemical fertilizer with bio-organic fertilizer and adding soil conditioners both reduce the intensity and total amount of soil N₂O gas emissions. However, the most significant reduction in emissions is achieved by reducing nutrient input through the application of 80% of the recommended formula fertilizer, which also reduces the risk of soil nitrate nitrogen leaching losses. Replacing 20% of the chemical fertilizer with bio-organic fertilizer significantly increases the yield of wheat and corn. In the third rotation season, the total yield of wheat and corn was significantly increased by 9.63% (P<0.05); combining 20% bio-organic fertilizer replacement with biochar can reduce the risk of nitrate nitrogen leaching into the 100–400 cm soil layer and significantly increases corn yield by 12.15%.