Abstract: The Jianghan Plain is a major rice-producing region in southern China. Long-term continuous rice cropping and high-frequency tillage have led to the degradation of soil aggregate structure, weakening the physical protection of organic carbon and accelerating its mineralization and loss, thereby constraining the sustainable improvement of soil fertility and the realization of farmland carbon sequestration potential. Investigating the effects of different planting modes of perennial rice varieties on soil aggregate stability and soil organic carbon can provide a theoretical basis for optimizing farmland tillage management practices and promoting soil carbon sequestration and emission reduction in the Jianghan Plain. A field experiment was conducted in Jingzhou City, Hubei Province in 2024, using a split-plot design. The main plots consisted of two “one planting, two harvests” planting modes (i.e conventional and mowing modes), and the subplots included two perennial rice varieties ‘Yunda 25’ (PR25) and ‘Yunda 109’ (PR109), and two ratoon rice varieties ‘Fengliangyouxiang 1’ (FLY) and ‘Yexiangyouyousi’ (YXY). By determining soil aggregate fractions and soil organic carbon content in the surface layer (0–20 cm) and subsurface soil layer (20–40 cm), the relationships among aggregate stability, belowground carbon input, and soil organic carbon under different planting modes and rice varieties were analyzed. The results were showed as below. Under the mowing mode, compared with planting ratoon rice varieties (FLY and YXY), organic carbon content in >2 mm aggregates, mass percentage of >2 mm aggregates, soil organic carbon content, and the mean weight diameter of aggregates with planting PR109 (the perennial rice variety) significantly increased by 20.99%–142.50%, 7.03%–22.90%, 22.00%–124.63%, and 5.05%–17.10%, respectively, for both surface and subsurface soil layer, while the soil erodibility factor decreased significantly. Under conventional mode, the effect of planting PR109 on various soil indicators in subsurface soil layer were generally higher than that in surface soil layer. Under conventional and mowing modes, the belowground carbon input with planting perennial rice varieties (PR25 and PR109) was 33.84%–80.49% higher than that with planting ratoon rice varieties (FLY and YXY). In the surface soil layer, soil organic carbon content was significantly correlated with belowground carbon input (P<0.01), indicating that increased belowground carbon input facilitated the accumulation of soil organic carbon. Soil aggregate stability indicators (geometric mean diameter of aggregate and mean weight diameter of aggregate) were signicantly negatively correlated with the soil erodibility factor (K). This suggests that aggregate structure plays an important regulatory role in soil erosion resistance. In conclusion, the perennial rice variety PR109 can significantly improve soil aggregate stability and soil organic carbon content, and combining it with the mowing mode can further enhance soil and water conservation and carbon sequestration benefits.