Abstract: Globally, approximately 10–20% of grasslands exhibit shrub encroachment phenomenon. This process alters vegetation composition, soil structure, and nutrient cycling, thereby affecting soil aggregate stability and exerting significant impact on the structure and function of grassland ecosystems. In this study, three shrub-encroached meadow ecosystems (Caragana erinacea, Sibiraea angustata, Dasiphora fruticosa) in Qinghai-Tibet Plateau were selected as the research objects, and soil samples were systematically collected from the 0–10 cm layer. Based on the combination of field sampling and laboratory experiments, combined with chemometric methods and multivariate statistical models, the aggregate stability and distribution characteristics of soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) in aggregates were analyzed. The results were as follows: after shrub encroachment, the content of >2 mm aggregates, water-stable aggregate (WSA) content, mean weight diameter (MWD), and geometric mean diameter (GMD) was significantly decreased in D. fruticosa-encroached plots, while these parameters were generally increased in C. erinacea-encroached and S. angustata-encroached plots. Aggregate destruction rate (PAD) in 0.25−2.0 mm size fraction was significantly decreased in C. erinacea-encroached plots but increased in S. angustata-encroached plots. Shrub encroachment significantly increased SOC and TN content in >2 mm and 0.25−2.0 mm aggregate fractions in C. erinacea-encroached plots. After shrub encroachment, TP content in <0.25 mm particle size fraction was significantly increased in D. fruticosa-encroached plots, while TN content in 0.25−2.0 mm fraction was significantly decreased. Correlation analysis indicated that MWD and GMD showed significant positive correlations with SOC and C:P ratio, while PAD exhibited significant negative correlations with nutrient indicators. These findings indicated that shrub encroachment could influence soil structural stability by regulating soil aggregate composition and nutrient distribution patterns, though the direction and intensity of these effects vary significantly among different shrub types. This study provides scientific evidence for elucidating soil ecological effects of shrub encroachment in alpine meadows and for ecological restoration of degraded grasslands.