Owing to extensive bedrock exposure and complex surface/underground geological structures, long-term farmland abandonment in karst regions is significantly more spatial heterogeneity than that in non-karst regions. Furthermore, the dynamics of soil total carbon (TC), total nitrogen (TN), and total phosphorus (TP) storage in different soil aggregate sizes, especially under different rocky desertification grades, remain unclear in karst trough valley after the farmland abandonment. Therefore, we examined the changes in soil aggregate size and stability, soil microbial biomass, and soil aggregate-associated TC, TN, and TP storage in cultivated farmland that had been abandoned for 0, 5, 10, 20, and 30 years under three rocky desertification grades (potential, mild, and moderate) in karst trough valley of China. Compared with cultivated farmland, abandoned farmland had greater proportions of minor and microaggregates and greater aggregate stability. Long-term abandonment (30 years) significantly increased the soil aggregate stability and soil microbial biomass-associated C, N, and P contents. Moreover, the highest C:N and C:P ratios were found in macro-aggregates from the moderately rocky desertification of cultivated farmland. Soil aggregate-associated TC (8171.76 g center dot m2-) and TN (46.66 g center dot m2-) storage was highest in moderate rocky desertification of cultivated farmland, whereas soil aggregate-associated nutrient storage was lowest in mild rocky desertified farmland that had been abandoned for 10 years. According to the structural equation models, the duration of farmland abandonment directly affects micro- aggregate nutrient storage, whereas the rocky desertification grade directly influences both minor- and micro- aggregate nutrient storage. These findings highlight the dynamics of soil aggregate-associated TC, TN, and TP storage during vegetation succession after farmland abandonment, and enhance our understanding of the interrelationships among soil nutrients and rocky desertification in karst regions.