Despite extensive research on soil organic carbon in karst regions, the synergistic changes in multiple carbon fractions and their stabilization mechanisms across a complete rocky desertification gradient remain poorly understood. To clarify how soil carbon pools and their drivers change during karst rocky desertification, we selected Kaiyuan City, Yunnan Province, China, as the study area. Total carbon (TC), soil organic carbon (SOC), and their related fractions, including particulate organic carbon (POC), mineral-associated organic carbon (MAOC), iron-bound organic carbon (Fe-OC), calcium-bound organic carbon (Ca-OC), and soil carbon isotopic composition (delta C-13), were analyzed under different degrees of rocky desertification. SOC and TC followed a nonlinear pattern: increasing from no to potential desertification, decreasing at light and moderate stages, and rising again at the severe stage, indicating a phased response rather than a monotonic decline. POC was lowest under no rocky desertification and increased significantly after desertification occurred, reaching its maximum at the severe stage. MAOC peaked at the potential stage. With increasing rocky desertification severity, POC/SOC increased from no to moderate stages and then slightly decreased, whereas MAOC/SOC generally decreased. Fe-OC and Ca-OC were lowest under no desertification and increased after desertification occurred, pointing to enhanced mineral protection. Soil delta C-13 values under moderate and severe desertification were higher than under no, potential, and light desertification, implying intensified decomposition and a relative increase in C-4 plants. Mean weight diameter (MWD) and geometric mean diameter (GMD) did not differ significantly among rocky desertification stages (p > 0.05). In contrast, fractal dimension (FD) differed significantly only between the light and moderate stages (p < 0.05). Correlation and redundancy analyses showed that soil water content, bulk density, and porosity were the key factors driving variation in SOC and its fractions. These findings provide both a theoretical basis and practical guidance for soil restoration and ecological management in karst faulted basins affected by rocky desertification.