Abstract: Aggregates are the crucial building blocks to form the foundation of soil structure for better soil stability. Moreover, the pore structure of aggregates can pose a great impact on the transport and distribution of solutes and gases, particularly on bioactivity and hydraulic characteristics. Many biotic and abiotic factors can also influence the pore system of soil aggregates. It is difficult to detect the pore structure at the aggregate level so far. The abiotic measures can also be one of the most important steps to determine the soil pore structure in recent years. However, there is still a relatively large current controversy on the effects of different long-term fertilization on the soil microstructure characteristics (porosity, pore size distribution, and tortuosity) and stability, due mainly to the different types of soils, fertilizer, crops, and tillage. Fortunately, a variety of Computed Tomography (CT) techniques combined with image analysis can provide the three-dimensional (3D) distribution of porosity and pore size for better investigation of the 3D microstructure of soil aggregates. Synchrotron-based X-ray micro-CT (SR-μCT) can be another excellent tool for the higher resolution, stronger contrast, and faster scanning speed during characterization. The objective of this study was to evaluate the impacts of long-term different patterns of fertilization (no fertilizer, inorganic fertilizer, and combination of organic and inorganic application) on the aggregate microstructure of the cinnamon soil aggregates in the cropland of North China using SR-μCT measurements. The soil aggregates with diameters of approximately 3-5 mm were collected from the cinnamon soil with a long-term fertilization trial established in 1992. Three types of soil aggregate samples (3-5 mm) within 0.10 m soil profiles were selected from each site and then were scanned at 4 μm voxel resolution with the Shanghai Synchrotron Radiation Facility (SSRF). The 3D pore structure was constructed to quantify using the digital image analysis software ImageJ. The locally adaptive thresholding was employed to segment the sub volumes in ImageJ software, where the thresholds were chosen using visual observation. The sub volume of 500×500×500 (voxel) was extracted to reduce the edge artifacts for further morphological analysis. A systematic evaluation was made of the aggregate water stability and the soil properties. The results showed that there were substantial changes in the pore microstructure and stability of soil aggregates in the study area after 26 years of different soil fertilization treatments. Among them, the indexes of soil aggregate porosity, large porosity, narrow porosity, average pore diameter, average tortuosity, average surface area of pore throat, and Average Mass Diameter (MWD) increased by 23.84%, 145.71%, 21.43%, 37.16%, 21.3%, 51.12% and 59.26%, respectively, during the long-term chemical fertilizer combined with organic fertilizer (OF) treatment, compared with the no fertilizer (CK). It infers that the long-term OF treatment significantly improved the microstructure and stability of the OF soil aggregates. As such, the surface runoff was easily infiltrated into the ground to relieve the impact on the soil matrix, thus making the soil structure more stable. There were similar microstructural characteristics and stability OF soil aggregates under long-term chemical fertilizer (NPK) and CK treatment, but significantly different from that under OF treatment. The finding can greatly contribute to quantifying the structure of the unique soil in the North China Plain. The different effects of diverse long-term fertilization measures on soil structure can also provide strong support to the agricultural soil quality evaluation and protection.