Fertilization practices are vital for agricultural productivity and soil health. However, the impact of long-term organic and inorganic fertilization on pore structure and related functions in paddy soil is still underexplored. In this study, macroaggregates approximately 5 mm in diameter were collected from a 20-year longterm experiment with no fertilization (CK), and those treated with chemical fertilizer (NPK), organic fertilizer (RS), and a combination of both (RS+NPK). The pore structure of these macroaggregates was examined using synchrotron radiation-based X-ray tomography, alongside a pore network model and skeleton analysis. The soil functions concerning the pore structure at the aggregate scale were assessed through their physical and topological properties. Results indicated that the pore structure of the macroaggregates responded differently to organic versus inorganic fertilization. Specifically, the application of NPK significantly reduced the connected porosity, accessibility, and network complexity within the macroaggregates, whereas the opposite effects were observed with the RS treatment. Connectivity analysis showed that the critical pores in CK, NPK, and RS+NPK treatments originated from plant roots, while those in the RS treatment were likely formed through the decomposition of rice straw. Compared to CK, the NPK treatment exhibited fewer channels with high hydraulic conductance, indicating impaired transportability of water and nutrients under saturated conditions, while the opposite was true for the RS treatments. Furthermore, skeleton analysis highlighted that the NPK treatment has fewer paths for preferential and capillary flow compared to CK, indicating reduced accessibility of air, water, and nutrients under unsaturated conditions. These findings are essential for understanding the changes in soil functions related to pore structure following organic and inorganic fertilizer applications and for optimizing fertilization strategies to preserve soil structure and health.