Aeolian sandy soils are typically characterized by low organic matter content and loose structural stability, which severely restrict soil carbon sequestration capacity and farmland productivity. Soil aggregates are the primary carriers and protective barrier for soil organic carbon (SOC), dominating the processes of SOC accumulation and stabilization. Long-term fertilization is a critical field management strategy for regulating soil structure and carbon sequestration; however, the way in which both applying organic fertilizer alone or in combination with mineral fertilizer mediate aggregate distribution, structural stability, and aggregate-associated SOC sequestration in aeolian sandy soils under continuous peanut monoculture conditions remains largely unexplored. This study was based on a 16-year continuous field fertilization experiment conducted on aeolian sandy soil in Northeast China. The experimental treatments included: CK (control, no fertilization), NPK (balanced mineral fertilization), M (organic fertilizer alone), and MNPK (a combination of organic and mineral fertilizers). The topsoil samples (0–20 cm) were collected after the peanut harvest. The aggregate was classified into four fractions using the wet-sieving method: coarse macro-aggregate (>2 mm), fine macro-aggregate (0.25–2 mm), micro-aggregate (0.053–0.25 mm), and the silt–clay fraction (0.25 mm) and enhanced the soil aggregate stability. The addition of manure resulted in significantly better effects than the application of mineral fertilizers alone. In comparison with the CK, SOC stocks in the NPK, M and MNPK treatments increased by 18.3%, 44.9%, and 65.5%, respectively. The SOC stock (9.3 Mg·ha⁻¹) and peanut yield were highest under the MNPK treatment. With equal exogenous manure-carbon inputs for the M and MNPK treatments, a strong organic–mineral synergistic effect was observed in the MNPK treatment. This synergy reinforced the sequestration of exogenous organic carbon. Correlation analysis confirmed that SOC sequestration in aeolian sandy soil was predominantly governed by macroaggregate formation and internal carbon enrichment, rather than changes in microaggregate and silt–clay fractions. Our results reveal that combined organic–mineral fertilization effectively facilitates macroaggregate formation, improves aggregate stability and enhances organic carbon sequestration in macroaggregates of aeolian sandy soils, while increasing crop yield. Hence, organic–mineral combined fertilization is a promising agronomic practice for soil improvement, carbon sequestration and sustainable production in aeolian-sandy peanut cropping systems, offering practical field references for low-carbon sustainable management of sandy farmland.