Fertilization alters crop yield, soil aggregation, and carbon sequestration potential. However, the specific effects and interactive mechanisms of long-term fertilization on soil organic carbon (SOC), aggregate-associated organic carbon (OC), and yield in dryland wheat fields remain poorly understood. Therefore, a field experiment with local farmer fertilization (NP), measured and controlled fertilization (NPK), chemical fertilizer plus organic fertilizer (NPKM), chemical fertilizer plus bio-organic fertilizer (NPKB), and no fertilizer (CK) was conducted for 10 years in a semi-arid region of China. We examined the characteristics of crop yield, SOC stock, and soil aggregate under different fertilization methods to explore the carbon sequestration mechanisms associated with increased yield. The results revealed a significant positive linear correlation between carbon sequestration and carbon input, with a carbon sequestration efficiency of 27.4%. Different fertilization treatments increased the proportion of macroaggregates (>0.25 mm) and significantly improved the water stability of soil aggregates, with the combined application of organic–inorganic fertilizers (NPKM and NPKB treatments) showing the most pronounced effect. A redundancy analysis revealed that carbon input was the most important factor affecting aggregate stability. Partial least squares path modeling revealed that SOC content was enhanced primarily because of the increase in macroaggregate-associated OC and carbon input, which in turn led to higher wheat yields. Our findings indicate that macroaggregate-associated OC and carbon inputs have significant implications for SOC sequestration in dryland fields. Thus, we suggest the integrated application of organic fertilizers with balanced NPK fertilizers to promote SOC accumulation, improve aggregate stability, and enhance crop yield.