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 and accelerating the mineralization and loss of organic carbon, 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 with a split-plot design in Jingzhou City, Hubei Province, 2024. 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 soil layer (0–20 cm) and subsurface soil layer (20–40 cm), we analyzed the relationships among aggregate stability, belowground carbon input, and soil organic carbon under different planting modes and rice varieties. The results are summarized as below. Under the mowing mode, compared with planting ratoon rice varieties (FLY and YXY), planting PR109 (the perennial rice variety) significantly increased organic carbon content in >2 mm aggregates, mass fraction of >2 mm aggregates, soil organic carbon content, and the mean weight diameter of aggregates 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 layers, while significantly decreased the soil erodibility factor. Under the conventional mode, the effects of planting PR109 on various soil indicators in subsurface soil layer were generally higher than those in surface soil layer. Under both conventional and mowing modes, the belowground carbon input of planting perennial rice varieties (PR25 and PR109) was 33.84%–80.49% higher than that of planting ratoon rice varieties (FLY and YXY). In the subsurface soil layer, soil organic carbon content was extremely significantly positively correlated with belowground carbon input (P<0.01), indicating that increased belowground carbon input facilitated the accumulation of soil organic carbon in the subsurface soil layer. Soil aggregate stability indicators (geometric mean diameter of aggregates and mean weight diameter of aggregates) were significantly negatively correlated with the soil erodibility factor. This suggests that aggregate structure plays an important regulatory role in soil erosion resistance. In conclusion, compared with planting ratoon rice varieties, planting the perennial rice variety PR109 can 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.