Soil aggregation can be substantially affected by fertilizers and contributes to soil organic carbon (SOC) sequestration in agroecosystems. However, the mass and C distributions in different aggregates in responses to fertilization regimes are not often synchronous, which may largely affect soil C storage and stability. We conducted a meta-analysis of 2440 paired observations from 63 publications to assess the fertilization effects (i.e. inorganic, organic, and their combinations) on soil aggregation and aggregate-associated OC, as well as their linkages to the stimulated bulk soil C. Overall, fertilizer application significantly increased the mean weight diameter of soil aggregates by 27.8%. The proportion of large (> 2mm) and small (0.25-2mm) macroaggregates were significantly increased by 19.8% and 17.2%, and that of microaggregate (0.053-0.25mm) and silt-clay fraction (< 0.053mm) were significantly decreased by 6.0% and 18.4%, respectively. In contrast, fertilization significantly increased C concentration in all aggregates. Organic fertilizer applications had remarkably greater effects than inorganic fertilizer applications on soil C concentration but the effects declined with decreasing aggregate size (from 36.5% to 13.2%), while that of inorganic application changed very little among aggregates (from 14.1% to 10.0%). The fertilizer effects on soil aggregation and aggregate-associated OC divergently responded to the gradients of major agronomic conditions (i.e. climate, soil properties, and duration). Organic fertilizer applications tended to have distinctly greater promotion effect than solely inorganic fertilizer applications with temperate climate, neutral-to-alkaline pH and more sand-like texture of soil. The importance of mineral- rather than larger size aggregate-associated OC in contributing to the bulk SOC pool tended to increase in the long term. The inorganic-organic combinations exhibited the most lasting effect on SOC accrual. In conclusion, the responses of bulk soil C to fertilizer applications were not always in accordance with those of soil aggregation, but can be well explained when jointly considering soil aggregate C. Our findings highlight the varying contributions of aggregates to the soil C pool in diverse and complicated agronomic situations, which are important to the agricultural C sink stability.