In order to characterize 3-D microstructures of the soil aggregates in the paddy soil of a long-term fertilization experiment on red soil in Jinxian, Jiangxi Province, as affected by different patterns of fertilization (CK, NPK and NPKOM), soil aggregates, 3~5 mm in diameter, collected from the paddy soil, were scanned with a micro-CT scanner at the Shanghai Synchrotron Radiation Facility (SSRF) for slice images, 3.7 μm in resolution, which were then processed with the 3DMA_Rock software into digital images for construction of a pore-throat network model. Results show that compared with CK, Treatment NPK decreased soil porosity, specific surface area, throat numbers, and average path length by 31.6%, 28.8%, 15.1% and 12.6%, respectively, while Treatment NPKOM increased them by 77.6%, 68.4%, 182.8% and 14.4%, respectively, demonstrating that long-term application of chemical fertilizer caused degradation of soil aggregate structure, whereas combined application of chemical fertilizer with organic manure significantly improved aggregate microstructure and promoted formation and stability of soil aggregates and the soil quality, thus keeping the soil in good aeration and permeability and building up soil fertility.