Biochar as agricultural soil amendment has been extensively investigated for its potential to sequester carbon, to mitigate greenhouse gases (GHGs) emissions, to enhance soil fertility and enhance crop yields. In this study, we investigated the impact of varying N fertilization rates in conjunction with biochar on soil properties, crop yield, and GHGs emissions in a rapeseed (Brassica napus L.)-soybean (Glycine max (L.) Merrill) rotation system for one year. Biochar and N fertilizer were applied following a factorial combination design of three biochar (B0: 0 t hm⁻², B1: 15 t hm⁻², and B2: 60 t hm⁻²) and three N fertilizer application rates (H: 100%, M: 75%, and L: 50% of the conventional application rates). In general, there was no significant effect of N fertilizer and its interaction with biochar application on soil water content, pH, and total carbon content, but the addition of biochar significantly increased these parameters (P < 0.05). The yield of both crops were significantly augmented by biochar up to 75% compared to using N fertilization alone, potentially due to enhanced N use efficiency. However, biochar significantly increased the cumulative N₂O and CH₄ emissions by as much as 2.2 times and 19 times, respectively, during the rapeseed season, thereby elevating the global warming potential (GWP) and the yield-scaled GWP. Nevertheless, the significantly increased soil carbon content following biochar addition might boost soil carbon sequestration, which could counterbalance the escalating GWP induced by GHGs. Therefore, we recommend a comprehensive and long-term evaluation of biochar's impact by considering crop yield, GHGs emissions, and carbon sequestration in agricultural systems to ensure sustainable agricultural management.