Helan Mountain is a typical forest ecosystem in the arid and semi-arid regions of China. In order to understand the mechanism of different altitudes on the stability of soil agglomerates and the change characteristics of organic carbon fractions with the change of altitude, the present study selected seven typical vegetation types within the range of 1300—2700 m in the Helan Mountain, and analyzed the physicochemical properties of soils, the characteristics of the distribution of the agglomerates and its stability in different elevations, and the mechanism of the change of organic carbon fractions of different grain sizes. We analyzed the physical and chemical properties of soils at different altitudes, the distribution characteristics of aggregates and their stability, and the mechanism of changes in organic carbon fractions in aggregates of different grain sizes. The study also revealed the driving factors affecting the changes in organic carbon in aggregates through correlation heat map analysis and redundancy analysis. The results showed that the water-stable agglomerates in the Helan Mountains mainly consisted of large agglomerates (>0.25 mm), and the content of large agglomerates and the stability of the agglomerates showed an increasing and then decreasing trend with the rise of altitude, and reached maximum at the poplar×turquoise hybrid at 2249 m. The results also showed that the organic carbon content and the stability of the agglomerates at different grain sizes at different altitudes showed an increasing and then decreasing trend with the rise of altitude. The soil organic carbon content of aggregates at different elevations increased gradually with the rise of elevation, and in general, the organic carbon in large aggregates was higher than that in micro-aggregates. The organic carbon oxidized fraction of agglomerates increased gradually with the rise of altitude, and the organic carbon content was mainly stored in large agglomerates, which reached the maximum value at the alpine meadow at 2617 m. The oxidative stability of organic carbon at middle and high altitudes (1968—2617 m) was significantly lower than that at low altitudes (1380—1650 m), and the organic carbon in large aggregates was easier to be oxidized and decomposed than that in micro-agglomerates and powdery clay particles. Organic carbon in large aggregates was easier to oxidize and decompose than that in microaggregates and powdery clay particles. Correlation analysis showed that soil organic carbon (SOC) 、elevation and total nitrogen (TN) were the main factors affecting the oxidative stability of organic carbon, and the factors of each component constrained each other. The principal component analysis showed that the soil physicochemical properties and aggregate stability coefficients contributed 62.25% and 21.60% to the organic carbon oxidation components. The results of this study has revealed the influencing factors on the stability of aggregates and the characteristics of organic carbon fractions at different altitudes in Helan Mountain, which is of great significance for the in-depth discussion of the storage of organic carbon and the stability of mountain forest ecosystems in Helan Mountain.