[Objective] A shallow karst fissure(SKF) is a significant habitat in rocky desertification areas that provides growing space, water, and nutrients for plant growth. To explore the differences in the stability of aggregates, the primary mechanism of aggregate decomposition in different soil horizons in SKF, and the vertical variation characteristics of nutrient contents in aggregates, an experiment was performed in the karst region of southwest China.[Method] Two typical forms of SKF (rectangle-type SKF and funnel-type SKF) was selected for this study and the particle size distribution and stability characteristics of soil aggregates in different soil horizons (0-20 cm, 30-50 cm, 50-70 cm, 70-90 cm, and 90-110 cm) were explored by the dry and wet sieving method. Also, the mechanisms of soil aggregate decomposition were analyzed by the Le Bissonnais method. Furthermore, the contents of soil organic matter (SOM), alkali-hydrolyzable nitrogen (AHN), and available phosphorous (AP) were determined in aggregates with different particle sizes, and the relationship between these nutrients and the stability of soil aggregates was analyzed.[Result] The aggregate fractal dimensions (D) under dry and wet sieving ranged from 1.57 to 2.18 and from 1.55 to 2.15, respectively. The stability and erosion resistance of SKF soil aggregates decreased with the depth of soil horizons, and the rectangle-type SKF soil aggregate was more stable than funnel-type SKF. The major mechanism observed for SKF soil aggregate decomposition was slaking generated by fast wetting. According to the indicators of percentage of aggregate disruption (PAD); the fractal dimension D and mean weight diameter (MWD), SKF soil aggregates have good water stability and permeability. In the 0-20 cm soil horizon, the variation of SOM, AHN, and AP contents in aggregates of different particle sizes were 38.34±6.53-90.91±10.02 g·kg^-1, 208.09±24.10-373.93±38.27 mg·kg^-1, and 1.98±0.96-8.13±6.45 mg·kg^-1, respectively. In soil 30 cm below the surface, the contents of SOM, AHN, and AP declined sharply compared to those in 0-20 cm soil horizon, which were 13.27±0.94-37.53±3.47 g·kg^-1, 71.58±3.27-198.54±22.63 mg·kg^-1, and 0.15±0.03-0.38±0.10 mg·kg^-1, respectively; with a very low AP content. Importantly, the particle size of aggregates was not an important factor governing the nutrient content of the aggregates. Additionally, SKF morphology had different effects on the variations in SOM, AHN, and AP contents with soil depth. SOM content below surface 30 cm horizons in rectangle-type SKF was significantly decreased with increasing depth of SKF, while no significant difference was observed in funnel-type SKF. The variation trends of AP content with increasing SKF depth were consistent in rectangular and funnel-type SKF profiles, while there was no significant correlation between the variation trends of AHN content and SKF morphology. According to the correlation analysis, higher SOM, AHN, and AP contents indicated stronger water stability of the SKF soil aggregates.[Conclusion] The water stability of SKF soil aggregates is an important factor for these soils and decreases as the soil horizons deepen, with the major mechanism of soil aggregate decomposition being slaking generated by fast wetting. Also, the morphology of SKF showed varied effects on the variations of SOM, AHN, and AP content at different soil depth.