Karst riverine carbon export is jointly regulated by climate, topography, and ecological degradation/restoration. Clarifying the dominant controls on dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) across different section types, together with their underlying pathways, is essential for diagnosing watershed carbon processes and evaluating ecological restoration outcomes. Taking the Lijiang River Basin as a case study, this study integrates XGBoost-SHAP analysis with multi-group structural equation modeling (SEM) to disentangle the driver assemblages, directional responses, and direct-indirect effect chains governing DIC and DOC in three spatial groups of sampling sections: main-channel control sections, confluence-affected sections, and tributary sections. The results show that both DIC and DOC differ significantly among section types. XGBoost-SHAP analysis indicates that the key controls on DIC are primarily characterized by the joint constraint of topographic background and carbonate-weathering-derived solute signals, whereas the explanatory factors for DOC are relatively consistent across section types, being mainly regulated by external inputs and redox conditions. Multigroup SEM further reveals that DIC is produced predominantly through carbonate weathering. The influence of rocky desertification on DIC is exerted mainly indirectly, through alterations in carbonate weathering intensity and watershed solute supply, thereby generating section-dependent differences: its overall effect is suppressive in the main-channel and confluence-affected sections, but it can be promotive in tributary sections. DOC, by contrast, is chiefly controlled by the combined enhancement of allochthonous organic/solute inputs and intensified oxygen-consuming decomposition, and the direction of rocky desertification effects on DOC also varies among section types. These findings reveal the differential control mechanisms and spatial heterogeneity of DIC and DOC in karst watersheds, and provide a quantitative basis for section-specific carbon-process diagnosis and carbon export assessment under ecological management and restoration.