The topographies of soil erosion and deposition are critical factors that significantly influence soil quality, subsequently impacting the erodibility of soils in karst regions. However, the investigation into the effects of erosion and deposition topographies on soil erodibility across different stages of vegetation succession in karst trough valleys is still at a preliminary stage. Therefore, three distinct topographic features (dip slopes, anti-dip slopes, and valley depressions) were selected at erosion (dip/anti-dip slope) and deposition sites (valley) to investigate the spatial heterogeneity of soil physicochemical properties, infiltration capacity, aggregate stability, and erodibility in karst trough valleys. Additionally, five different stages of vegetation succession in karst forests were considered: Abandoned land stage (ALS), Herb stage (HS), Herb-Shrub stage (HES), Shrub stage (SHS), and Forest stage (FS). Additionally, the relationships among these factors were analyzed to identify the key driving factors influencing soil erodibility. The results revealed that soil physicochemical properties and soil aggregate stability at the deposition site were significantly superior to those at the erosion site. The FS resulted in the best soil physicochemical properties, whereas the HS resulted in the highest soil aggregate stability within the deposition site. However, the soil infiltration capacity at the erosion site was significantly greater than that at the deposition sites. The ALS had the strongest soil infiltration capacity at both the erosion and deposition sites. The soil erodibility at erosion sites (0.064) was significantly greater than that at deposition sites (0.051), with the highest soil erodibility observed on anti-dip slopes during the HES at erosion sites (0.142). The structural equation model reveals that erosion and deposition topographies, vegetation succession, soil physicochemical properties, soil aggregates, and soil infiltration characteristics collectively account for 88% of the variation in soil erodibility under different conditions. Specifically, both direct and indirect influences on soil erodibility are most significantly exerted by soil aggregate stability and vegetation succession. This study provides scientific evidence to support the management of soil erosion and ecological restoration in karst trough valleys while offering technical assistance for regional ecological improvement and poverty alleviation.