Leguminous green manure plays a vital role in improving soil quality and enhancing soil carbon sequestration within agricultural ecosystems. This study focused on young rubber plantations in Hainan and employed five treatments: Pueraria phaseoloides (Roxb.) Benth. (GT), Tephrosia candida DC. (SMD), Stylosanthes guianensis (Aubl) Sw. (ZHC), Crotalaria pallida Ait. (ZSD), and weed control (CK). We measured soil water-stable aggregates and soil organic carbon (SOC) content at the 0-20 cm and 20-40 cm depths using wet sieving and potassium dichromate heating methods and further analyzed the relationships of aggregate stability and SOC. Compared to that under the CK treatment, the SMD covering treatment significantly increased SOC at depths of 0-20 cm and 20-40 cm by 19.8% and 25.3%, respectively. The GT covering treatment also significantly increased SOC in the 20-40 cm layer by 26.7%, while the ZHC and ZSD treatments had no significant effect on the SOC in either soil layer. The GT and SMD treatments significantly improved the aggregate stability indicators [mean weight diameter (MWD) and geometric mean diameter (GMD)], the proportion, and SOC associated with >2 mm size aggregates, while the ZHC and ZSD treatments markedly reduced the MWD and GMD in the 20-40 cm soil layer, as well as the proportion of >2 mm size aggregates. The GT treatment significantly enhanced the SOC enrichment coefficients of 0.25-2 mm size aggregates in the 0-20 cm soil layer and 1-2 mm size aggregates in the 20-40 cm soil layer. The SMD treatment also substantially increased the SOC enrichment coefficient of 1-2 mm size aggregates in the 20-40 cm soil layer. Both the GT and SMD treatments notably improved the contribution rate of SOC from >2 mm size aggregates by 65.7% and 105.5% in the 0-20 cm layer and 58.6% and 79.1% in the 20-40 cm layer, respectively, while significantly reducing the contribution rate of SOC from < 0.25 mm size aggregates. Spearman correlation analysis revealed a significant positive correlation between the total SOC and MWD and GMD of aggregates at both depths of 0-20 cm and 20-40 cm. In summary, GT and SMD coverings in young rubber plantations can enhance the proportion of soil macro-aggregates, increase organic carbon content, and improve the stability of soil aggregates. The findings provide a theoretical basis for implementing perennial green manure covering practices in the tropical rubber plantation regions, as well as for enhancing soil fertility and erosion control.