To investigate the effects of long-term fertilization and organic material application on black soil aggregate structure, this study was based on a long-term field experiment at the National Field Scientific Observation and Research Station in Hailun, Heilongjiang Province, China. Four treatments were selected: no fertilization (CK), chemical fertilizer alone (NPK), chemical fertilizer combined with straw return (NPKS), and chemical fertilizer combined with organic manure (NPKM). Aggregate size distribution and stability under long-term fertilization were analyzed, and synchrotron radiation micro-CT scanning combined with three-dimensional image analysis was employed to systematically examine the effects of different fertilization practices on the pore structure of 3-5 mm black soil aggregates. The results showed that, compared with CK, fertilization significantly promoted the formation of >2 mm and 0.25-2 mm aggregates, increasing them by 22.5%-79.0% and 31.5%-50.6%, respectively. Fertilization also significantly increased total porosity, specific surface area, pore throat density, pore density, and connected pore density of aggregates. Among the fertilization treatments, total porosity, specific surface area, and pore connectivity under NPKS were significantly higher than those under NPK, while all pore structural parameters under NPKM were the highest and significantly exceeded those under both NPK and NPKS. Compared with CK, fertilization significantly promoted the formation of pores >50 µm; NPK mainly enhanced the formation of 50-200 µm pores, increasing them by 33.4%-53.2%. Compared with NPK, NPKS and NPKM significantly promoted the formation of pores >100 µm and increased aggregate aeration porosity by 36.4%-170.4% and 62.7%-509.9%, respectively. Elongated pores were the dominant pore shape in black soil, and fertilization significantly increased both elongated pore porosity and its proportion in total porosity, following the order NPKM > NPKS > NPK among the three fertilization treatments. Correlation and random forest analyses indicated that pore structural parameters had significantly greater explanatory power for aggregate stability than basic soil physicochemical properties, with total porosity, macroporosity, specific surface area, and connectivity characteristics identified as the key factors affecting aggregate stability. In conclusion, long-term combined application of organic materials with chemical fertilizer, especially under the NPKM treatment, can significantly optimize the pore structure of black soil aggregates, enhance their connectivity and stability, and provide important pore-scale evidence for black soil structural improvement and cultivated land quality enhancement.