Understanding how fresh, decomposed, and root-derived particulate organic matter (POM) interact with soil macropores is crucial for enhancing soil organic carbon stocks, yet their spatial relationships remain largely unclear. Therefore, we conducted an 8-year conservation tillage experiment on a Vertisol (wheat-maize rotation, no tillage with straw return) that compared four fertilization regimes: (i) control (no fertilization), (ii) chemical fertilization (NPK), (iii) organic fertilization (OF), and (iv) combined chemical-organic fertilization (NPKOF). X-ray computed tomography was used to quantify POM fractions, macropore and biopore structure. Our results demonstrated that all fertilization treatments (NPK, OF, NPKOF) significantly improved soil macropore structure in the 0–10 cm layer, whereas OF and NPKOF increased bioporosity by 4.82-fold and 2.26-fold in the 10–20 cm layer (P < 0.05). Biopores constitute a major component of percolating pores in the subsoil and are promoted by the application of organic fertilization. Furthermore, OF and NPKOF significantly enhanced fresh POM and root-derived POM content in the 0–10 cm layer and shortened their distance to pores throughout the 0–20 cm layer (P < 0.05). The three POM fractions exhibited positive correlations with macropore structure characteristics (P < 0.05), yet no significant correlation was observed between root-derived POM and biopores. Root-derived POM showed preferential accumulation in areas distant from biopores. Overall, our findings demonstrate that long-term organic fertilization is linked to increased POM accumulation, improvements in surface soil macropore structure, and enhanced biopore formation in the subsoil of Vertisols.