In order to investigate the influence of karst microhabitat types on the stability of soil aggregates and to reveal main destabilization mechanisms of soil aggregates in microhabitats, five typical microhabitats in the study area, namely stone crevices, stone ditch, stone sink, stone and earth surfaces, and earth surface are selected. The dry sieve method, Elliott wet sieve method, and Le Bissonnais method are used to determine the stability of soil aggregates. The results show that after wet sieving, the distribution of agglomerates is dominated by water-stable agglomerates (WR_>0.25) with a content of over 81.26%, the percentage of aggregate destruction(PAD) ranged from 8.93% to 17.39%, the mean weight diameter(MWD) ranged from 1.94 to 2.85 mm, all smaller than the MWD of the dry sieving method, and the stability of the agglomerates shows that the stone sink is the best, the earth surface is the worst, and stone and earth surfaces is the second worst. The trend of MWD values after Le Bissonnais method treatment is slow wetting (SW) > pre-wetting and strirring (WS) > fast wetting (FW), indicating that the maximum damage mechanism of soil agglomerates in microhabitats is the dissipative effect of fast wetting FW during heavy or stormy rainfall, and the stability of the agglomerates is shown to be best in the stone sink, worst in the earth surfaces and stone and earth surfaces is the second worst. Correlation analysis shows that the MWD determined by the Le Bissonnais method are all significantly positively correlated with WR_>0.25 for the wet sieve method and negatively correlated with PAD (P<0.05), indicating that the Le Bissonnais method and the wet sieve method have good correlation and that the Le Bissonnais method is feasible for determining the stability of soil aggregates in karst areas (P<0.05). The MWD under the FW treatment in the Le Bissonnais method is significantly positively correlated with organic matter, indicating that organic matter has an important effect on agglomerate stability; total N, total P and total K is significantly positively correlated with MWD under WR_>0.25 and SW treatments, and negatively correlated with PAD, indicating that a stable agglomerate structure has a positive effect on nutrient accumulation (P < 0.05). The results of the different measurement methods show that earth surface and stone and earth surfaces microhabitats are prone to soil erosion and that protection of them in karst ecologically fragile areas should be strengthened during the rainy season.