【Objective】The application of Chinese milk vetch to paddy soil is an effective practice to improve the 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 with 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 were shown that the soil aggregate content (>2mm) was dominant (the highest) and 61.12%~68.53%, followed by the 2-0.25mm. The application of Chinese milk vetch increased the percentage of the soil aggregate size (>2mm) by 5.93%~9.91%. The content of the organic carbon in >0.053mm aggregates and total nitrogen in aggregates were increased with the increase of the application of Chinese milk vetch. There were significant positive correlation between the content of organic carbon and total nitrogen and the application of Chinese milk vetch. The applications of Chinese milk vetch increased the total storage of organic carbon and nitrogen by 19.42%~37.09%and 22.31%~40.13%, respectively. The distribution of the organic carbon and nitrogen in >2mm soil aggregate was increased by the application of Chinese milk vetch. The relative content of the aliphatic organic carbon and aromatic organic carbon in soil aggregates were increased with the application of Chinese milk vetch by the FTIR spectroscopy. And there were significant positive correlation between the N-H functional groups and the application of Chinese milk vetch. The application of Chinese milk vetch increased the values of the relative intensity of 1630/2850+2940 and 1720/2850+2940 in different soil aggregates to improve the physical protection on the organic carbon. There were significant positive correlation between the values of the relative intensity of 1630/2850+2940 in both aggregate sizes of >2mm and 2-0.25mm and the application of Chinese milk vetch.【Conclusion】Hence, the application of Chinese milk vetch incorporated improved the distribution of paddy soil aggregates and increased the activity and the stability of organic carbon and the organic carbon and nitrogen storage in soil aggregates to enhanced the paddy soil fertility.