The soil porosity and pore size distribution are useful indicators for understanding the impact of fertilization practice on soil quality. In this study, a combined approach of nitrogen gas adsorption (NA), mercury intrusion porosimetry (MIP) and synchrotron radiation X-ray computed microtomography (SR-mCT) was used to study the impact of mineral and organic fertilization on the pore structure in aggregates of paddy soils (porosity, pore size distribution, pore morphology, and pore network). The paddy soil was treated with long-term mineral and organic fertilization (control (CK), chemical fertilizers (NPK), pig manure (PM), and pig manure plus chemical fertilizers (PM + NPK)) under rice-wheat cropping system. The total pore volume estimated by NA method was significantly (p > 0.05) lower in PM than in NPK and CK treatments. The PM treatment significantly increased the total pore volume (TPV) determined by both MIP and SR-mCT methods, while the NPK treatment showed no statistically significant difference relative to the CK treatment. The long-term fertilization greatly affected soil pore size distribution, particularly PM treatment increasing the volumes of macro-, meso-, and micropores, while decreasing the volumes of ultramicro- and cryptopores. The PM treatment significantly increased degree of anisotropy (DA), and elongated pore fraction, and decreased regular pore fraction compared with the CK treatment, while the NKP treatment no significant difference. The NPK and PM treatments significantly affected pore network structure, PM treatment increasing throat area, channel length, key node pores, path length, and network diameter compared with CK treatment, while the verse was true for the NPK treatment. The 3D SR-mCT visualization on aggregates revealed that mineral and organic fertilization affected the pore spatial distribution within the aggregate. The long-term application of mineral fertilizer would deteriorate pore structure by affecting the pore morphology and network structure. Our results was helpful for understanding the impact of fertilization practice on soil quality and illustrating the importance of pore network structure in evaluating the response of soils to fertilization management.