Abstract: Synchrotron based X-ray micro-computed tomography (SRμ-CT) can nondestructively capture images of the interior structure with high resolution and strong contrast, and is therefore an excellent tool to investigate the 3-D microstructure of soil aggregates. Aggregates with diameters around 5 mm were collected from paddy soils with rice cultivation for 20 and 40 years, respectively, and the aggregates were scanned with SRμ-CT at a resolution of 9 μm. Aggregate microstructure was visualized and quantified using digital image analysis method and 3DMA-Rock software. Results showed the SOM and total nitrogen content significantly increased after 40 years of rice cultivation compared with 20 years of rice cultivation. The number of pores, porosity, and the specific surface area of soil aggregate significantly increased with the increase of cultivation years. Aggregates of paddy soil with 20 years rice cultivation had a dense massive microstructure with few connected pores, while the aggregate with 40 years rise had a more heterogeneous porous microstructure. The results indicated significant improvement of aggregate microstructure and soil quality with the increase of rice cultivation years.