This study hypothesized that long-term fertilization alters the pore structure and aggregate stability in upland red soil. A long-term fertilization experiment in Qiyang, Hunan, was conducted with three treatments: no fertilization (CK), nitrogen–phosphorus–potassium fertilization (NPK), and nitrogen–phosphorus–potassium combined with pig manure (NPKOM). X-ray computed tomography (CT) scanning technology was used to assess three-dimensional pore structures at both the soil column (50 mm diameter and 50 mm height) and aggregate scales (diameter 3–5 mm), alongside the evaluation of the soil’s physical and chemical properties. Results showed that the soil organic carbon content (SOC) increased by 44.8% in NPK and 112.5% in NPKOM compared to CK. NPKOM improved the aggregate stability by 51.6%, whereas NPK had no significant effect. At the soil column scale, NPK increased the total porosity by 13.7% but reduced larger pores (>0.06 mm), whereas NPKOM decreased the total porosity by 7.8% and increased larger pores. At the aggregate scale, NPKOM increased the porosity for pores >0.098 mm by 7.6 times compared to CK and 9.5 times compared to NPK. In conclusion, long-term NPKOM significantly enhances the SOC and aggregate stability and promotes larger pore formation, unlike NPK, which mainly increases SOC but does not improve the soil structure.