Soil aggregates, as fundamental units of soil structure, play a crucial role in promoting the storage of soil carbon and nitrogen, thereby supporting soil fertility and overall health, especially in fragile karst regions. However, the response of soil aggregate composition and associated carbon and nitrogen pools to different ecological construction measures in such areas remains unclear, particularly in relation to contour reverse-slope terrace practices. In this study, we evaluated the differences in the stability of soil aggregates (macroaggregates >2 mm, medium aggregates 2–0.25 mm, and microaggregates <0.25 mm) in sloping cropland and four ecological construction measures (contour reverse-slope terrace, fallow farmland reforestation, natural vegetation restoration, and meridian forest) in the Chishui River Basin of the karst region in Yunnan Province, China, as well as the relationship between carbon and nitrogen pools within the aggregates and the carbon and nitrogen sequestration potential of different treatments. Compared to sloping cropland, the contour reverse-slope terrace treatment, with its unique “preferential entrainment” function, significantly increased the content of medium and microaggregates by an average of 85.67%. Among the ecological construction measures, plantation forests exhibited the highest aggregate stability, with an average increase of 7.59%–157.14%. The carbon and nitrogen contents across all aggregate sizes were highest in microaggregates, which contributed most to the soil carbon and nitrogen pools in the study area. Natural vegetation restoration resulted in the highest carbon and nitrogen levels across all aggregate types. Moreover, the plantation forest and contour reverse-slope terrace treatments showed a balanced contribution of carbon and nitrogen within all aggregate sizes. Overall, these findings suggest that planted forests are the most effective in enhancing soil and water conservation in fragile karst areas. The contour reverse-slope terrace approach shows potential for stabilizing soil structure due to its unique “preferential entrainment” function over delayed time scales.