The aims were to study the effects of carbon-based organic fertilizer on the composition and stability of soil aggregates, and to determine the application effect of carbon-based organic fertilizer in the improvement and cultivation of red soil for tobacco growing and flue-cured tobacco production. Taking the typical tobacco-growing red soil in Panxi area of Sichuan Province as the research object, field experiments were conducted. The effects of control (CK), application of biochar (T₂), application of cow manure (T₃), 50% cow manure combined with 50% biochar (T₄) and 70% cow manure combined with 30% biochar (T₅) on soil aggregate composition and stability were determined. The results showed that with the growth period of flue-cured tobacco, the aggregate stability of red soil increased first and then decreased from <0.053 mm to 0.25-2 mm and 0.053-0.25 mm, and the 0.25-2 mm was the main concentration. In the mature stage of flue-cured tobacco, the aggregate content of 0.25-2 mm in the topsoil (0-20 cm) treated by T₄ and T₅ increased by 1.99-4.19 percentage points compared with T₂ and T₃, and the mean weight diameter (MWD) of aggregates increased by 4.41%-19.67%. Aggregate content greater than 0.25 mm (R_0.25) was increased by 4.67-17.57 percentage points. Redundancy analysis showed that soil organic matter content was positively correlated with aggregates of 0.25-2 mm and 0.053-0.25 mm, which was the main factor affecting the particle size distribution and stability of aggregates in red soil. Carbon-based organic fertilizer could increase the content of organic matter in tobacco-growing red soil, promote the formation of large aggregates, and improve the stability of aggregates.