The study aimed to investigate the differences in soil aggregate structures and organic carbon and nitrogen distribution under different years of citrus and soybean intercropping system in order to provide reference for orchard soil improvement. Four treatments were set up in the field positioning experiments, including clear tillage area (CK, citrus without soybean), citrus and soybean intercropping for 1 year (T1), 2 years (T2) and 3 years (T3), respectively, and then soil aggregate composition, stability, organic carbon and total nitrogen contents were determined and compared under the different treatments. The results showed that: 1) Compared with CK, the contents of large aggregates >0.25 mm increased by 19.58% to 22.29% under citrus and soybean intercropping treatments. 2) The stability characteristics of soil aggregates in citrus–soybean intercropping were as follows: T3>T2>T1>CK. 3) The contents of organic carbon and total nitrogen were the highest in > 5 mm aggregates, but the lowest in <0.25 mm aggregates, and the C/N ratios under citrus and soybean intercropping treatments increased by 1.16–1.19 times compared with CK. 4) The correlations were significant between soil aggregate composition and organic carbon and total nitrogen contents in soil aggregates. RDA explained 99.32% and 94.99% of difference information respectively, among which >5, 5 – 2 and 0.5 – 0.25 mm soil aggregates were the main environmental factors affecting the changes of soil organic carbon and total nitrogen contents. In conclusion, citrus and soybean intercropping system promotes soil fertility and soil aggregate structure, thus, it is a sustainable agricultural mode.