Long-term applications of inorganic and organic fertilizers have great effects on soil characteristics and crop yields. However, it is limited to quantify the influence of long-term fertilization on soil micro-pore structure. In this study, we investigated the effect of long-term fertilizer application on soil pore characteristics using X-ray computed tomography. Loess soil cores were collected from four 25-yr fertilization treatments in Guanzhong Plain, Northwest China, including no fertilization (CK), nitrogen alone (N), nitrogen + phosphorus + potassium (NPK) and organic manure + chemical fertilizer NPK (OMNPK). The results indicated that, compared with other treatments, OMNPK treatment significantly increased winter wheat (Triticum aestivum L.) yield, total porosity, soil organic carbon and total nitrogen, and decreased soil bulk density. Notably, there is greater soil pore connectivity (EuN, Euler number) and lower fractal dimension in OMNPK than other treatments. Pore size distribution showed a significant difference with different diameters in <50, 50-100, 100-1000, and >1000 μm. In contrast, pore shape distribution of soil core differed little among different treatments, while elongated shape pores were appropriately 99.5% at OMNPK with more frequency than other treatments. Co-application of organic and inorganic fertilizers improved soil pore structure and soil physical-chemical properties, which is beneficial for preventing soil degradation.