The maintenance and stability of soil structures are critical for the stability of alpine grassland ecosystems. To elucidate how soil structures are altered by the degradation of alpine grasslands, this study investigated the various characteristics of soil aggregate particle sizes, and associated interactions with soil variables and soil stability in lightly, moderately, and severely degraded alpine steppes and meadows in Tianjun County, Qinghai Province, China. The results revealed that grassland degradation culminated in the modification of soil particle sizes from macro-aggregates (2-0.25 mm) to microaggregates (0.25-0.053 mm), to silt + clay fractions (<0.053 mm), and the stability of soil aggregates decreased. Moreover, the finer particle size grade might more clearly reflect soil disaggregation processes. Soil organic carbon (SOC), soil total nitrogen (STN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) contents of both alpine steppes and alpine meadows significantly decreased with the worsening of grassland degradation. However, the microbial entropy carbon (qMBC) hardly changed, whereas the microbial entropy nitrogen (qMBN) of the severely degraded alpine steppes and alpine meadows were significantly higher than their counterparts in lightly and moderately degraded grasslands. Redundancy analysis (RDA) revealed that SOC, STN, MBC and MBN were positively correlated with the 2-1 mm fraction and the mean weight diameter (MWD) in both the alpine steppes and alpine meadows, but negatively correlated with the 0.25-0.1 mm fraction in the alpine steppes, and the <0.053 mm fraction in the alpine meadows. Structural equation model (SEM) results revealed that SOC and STN were the critical factors affecting the composition and stability of soil aggregates.