【Objective】The application of Chinese milk vetch to paddy soil is an effective practice to improve soil fertility and maintain high and stable yields in South China. The soil aggregates distributions and their carbon and nitrogen content may be influenced by the continuous multi-year application of Chinese milk vetch.【Method】We investigated the effects of 12 years of Chinese milk vetch returned to soil on soil aggregate size distribution and aggregate-associated carbon and nitrogen by setting with six treatments including CK (no fertilizers and no Chinese milk vetch applied), GM0 (fertilizer only) and four gradients of Chinese milk vetch applied (GM1-4). The aggregate size distribution and the content and storage of organic carbon and nitrogen in the soil aggregate were analyzed. Also the types and relative intensity of organic functional groups in different size classes were determined using Fourier Transform Infrared spectrometer (FTIR).【Result】The results showed that the >2 mm soil aggregate was dominant (61.12%～68.53%) and followed by the 2～0.25 mm fraction. The application of Chinese milk vetch increased the percentage of the soil aggregate size (>2 mm) by 5.93%～9.91%. Also, the contents of organic carbon and total nitrogen in the >0.053 mm aggregates increased with the application rate of the treatment. There was a significant positive correlation between the contents of organic carbon and total nitrogen and the application rates of Chinese milk vetch. Interestingly, the application of Chinese milk vetch increased the total storage of organic carbon and nitrogen by 19.42%～37.09% and 22.31%～40.13%, respectively. Moreover, the distribution of organic carbon and nitrogen in >2 mm soil aggregate was also increased after the treatment. FTIR spectroscopic analysis revealed that the relative contents of aliphatic and aromatic organic carbons in soil aggregates were increased after treatment, and there was a significant positive correlation between the N-H functional groups and the application rate of Chinese milk vetch. In addition, the relative intensities of 1 630/2 850+2 940 and 1 720/2 850+2 940 in different soil aggregates were increased. There was a significant positive correlation between the values of the relative intensity of 1 630/2 850+2 940 in both aggregate sizes of >2 mm and 2～0.25mm and the application of Chinese milk vetch.【Conclusion】The application of Chinese milk vetch to paddy soil improved the distribution of soil aggregates, increased the activity and stability of organic carbon, and enhanced the organic carbon and nitrogen storage in soil aggregates. These positive impacts of Chinese milk vetch played an important role in enhancing paddy soil fertility.