To explore the responses of soil aggregate composition and stability to different grazing intensities in alpine meadow of the Qilian Mountains, no grazing (CK) was set as the control, with four treatments including light grazing (LG), moderate grazing (MG), heavy grazing (HG) and extreme grazing (EG) established. The characteristics of soil aggregates in the 0–10 cm and 10–20 cm soil layers were determined by the dry sieving method and wet sieving method, and three stability parameters including the mean weight diameter (MWD), geometric mean diameter (GMD) and fractal dimension (D) were analyzed. Combined with environmental and biological factors, the mechanisms underlying the effects of grazing on soil aggregates structure and stability were elucidated. The results showed that: (1) Soil aggregates with the particle size of 5–10 mm were the dominant fraction in the soil structure of the alpine meadow, and this fraction changed drastically with grazing intensity. CK maintained relatively high aggregate mechanical stability but exhibited weaker resistance to water erosion compared to grazed plots. Under the CK condition, the content of water-stable aggregates with the 5–10 mm particle size decreased significantly compared with mechanical-stable aggregates (by 60.07% in the topsoil and 70.66% in the subsoil). Light and moderate grazing maintained a dynamic balance and high stability of soil structure. Heavy and extreme grazing intensified soil structure fragmentation and overall stability declined. (2) Soil aggregate stability was correlated with environmental factors. Altitude and soil bulk density were significantly positively correlated with aggregate stability (P<0.001).Root biomass exerted a significant effect on the stability indices of mechanically stable aggregates in the topsoil (P<0.05); high root biomass destroyed soil macroaggregates but enhanced the resistance to water erosion. Soil microbial biomass carbon (SMBC), nitrogen (SMBN), phosphorus (SMBP) were significantly positively correlated with GMD of water-stable aggregates, but negatively correlated with GMD, MWD and D of mechanical-stable aggregates, also MWD and D of water-stable aggregates. Nitrate nitrogen had a positive effect on aggregate stability, while ammonium nitrogen had a negative effect. (3) The stability of aggregate in different soil layer varied under different grazing intensity. Under LG and MG conditions, the subsoil exhibited higher aggregate stability than the topsoil, whereas the opposite pattern was observed under HG, EG and CK conditions. Therefore, from the perspective of soil structural stability and sustainable utilization, light and moderate grazing are the optimal utilization patterns for alpine meadow in the Qilian Mountains. It not only maintains the structural stability of subsoil aggregates but also balances biological cementation and physical disturbance, avoiding aggregate water stability insufficiency under no grazing and the risk of structural fragmentation under heavy or extreme grazing. The findings provide a scientific basis for rational grazing management and soil conservation in alpine meadow of the Qilian Mountains.