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Biochar application as an organic amendment has been practiced to reduce soil acidity, enhance nutrient utilization, and improve crop growth and yield. However, uncertainties remain about the long-term effects of organic amendment and chemical fertilizers under crop rotation to ensure the sustainability and conservation of soil fertility and nutrient requirements of crops. A three-year field trial of rice-rapeseed rotation was conducted to investigate the effects of biochar (0, 3, 9, 15, 30, and 60 t ha−1) coupled with compound fertilizer NPK (15-15-15) at the ratio (N: P: K 1:0.8:0.8) for rice and (N: P: K 1:0.5:0.5) for rapeseed. The results showed that biochar amendment consistently improved the soil physiochemical properties such as soil pH, soil organic carbon and soil total porosity, soil enzyme activities, nutrient uptake, and yield of rice and rapeseed compared to plots with no biochar. Compared to control, plots treated with biochar at 30 t ha−1 increased the activity of urease up to 52 % and 39 % and invertase by 15 % and 32 %, while biochar at 60 t ha−1 increased the activity of soil catalase by 34 % and 32 % and alkaline phosphatase by 35 % and 41 % respectively under rice and rapeseed cultivation in the last two years of the study. The findings of the study revealed that coupling of biochar 15 t ha−1 with compound fertilizer significantly improved the grain yield of rice by 12 % and rapeseed by 22 % in the first year, and biochar amendment at 30 t ha−1 improved rice yield by up to 14 % and 22 % and rapeseed up to18 % and 21 % in the last two years. However, compared to 15 and 30 t ha−1, 60 t ha−1 biochar was ineffective and reduced the nutrient uptake and yield throughout the study. The soil conditions, growth, and yield of rice and rapeseed were improved in control plots with no biochar in the last two years, indicating crop rotation's positive effect. Altogether, our findings suggest that crop rotation under the combined application of biochar and chemical fertilizer is a promising approach to ensure soil fertility and crop productivity on a long-term sustainable basis. • Chemical fertilization depleted soil's chemical and physical properties. • The nutrient capacity and delivery performance of organic fertilizer were insufficient. • Biochar promoted soil quality and compensated nutrient delivery of organic fertilizer. • Biochar with organic fertilizer under crop rotation enhanced nutrient utilization and crop production. [ABSTRACT FROM AUTHOR]