Red soils are characterised by acidic pH and limitations in carbon, nitrogen, water, and soil structure. To overcome such limitations, improved soil aggregation is the key to improving the physical and chemical properties of soil. Applying organic amendments such as straw can lead to corresponding soil aggregation and stability changes. Therefore, we explored the short-term effects of rice straw amendment, either alone or in combination with biochar, on improving the carbon fractions, stability, and composition of soil aggregates in red soil with a history of vegetable planting. The study consisted of four treatments: control (no organic material, CK), biochar alone (5% homemade straw biochar, B), straw alone (12% rice straw, S), and biochar with straw (5% homemade straw biochar + 12% rice straw, BS). Our results showed that equal amounts of straw and biochar substantially reduced the number of mechanically stable aggregates (MSA), mean weight diameter (MWD), and geometric mean diameter (GMD) of the soil. BS treatment reduced >0.25 mm aggregate content (R0.25), MWD and GMD by 24.06%, 56.81%, and 62.19%, respectively, compared with that of the control. The addition of straw greatly enhanced the water-stable macromolecular content and stability coefficient of the soil, but treatment B had no obvious effect. The S treatment had the greatest effect on R0.25, MWD and GMD, increasing them by 143.94%, 246.67%, and 181.82%, respectively, compared with that of the control. Soil organic carbon (SOC) was significantly increased by straw addition and carbonisation treatment, and the effect of the BS treatment was the best, with an increase of 325.63% compared with that of the control. The organic carbon content in the aggregates of different particle sizes treated with different organic materials also increased significantly. In the soil reactive organic carbon fraction, applying biochar alone did not affect microbial biomass carbon (MBC), dissolved organic carbon (DOC), or easily oxidized organic carbon (EOC) but could increase the particulate organic carbon (POC) content. All the treatments with straw application significantly increased the MBC, DOC, EOC, and POC content, and the highest effect was obtained by applying both straw and biochar in an integrated form, i.e., the BS treatment. In conclusion, the co-application of biochar and straw sequestered more carbon and revamped soil C pools than either biochar or straw alone and could be a promising option for the sustainable use of red soils to ameliorate the aforementioned limitations associated with this soil type.