Crop rotation of flooded rice with maize can help sequester more carbon in the soil. Adding biochar to the soil increased soil organic carbon levels and crop yields in both cropping systems. The maize-rice rotation with biochar had a higher carbon sequestration rate compared to continuous flooded rice. The 0.25–2 mm soil aggregates showed the most significant increase in carbon content with biochar addition. Overall, the maize-rice system with biochar led to higher productivity and environmental benefits.