Karst rocky desertification (KRD) is a process where strong anthropogenic disturbances and exposure of carbonate bedrock occurs in fragile karst ecosystems. The fractional cover of rocky outcrops is a key indicator and mechanistic driver of KRD and can be accurately assessed using remote sensing technology. Nevertheless, rugged karst terrain relief can cause shadow effects on satellite imagery and combine with high heterogeneity of karst landscapes to prevent fractional cover retrievals. In this study, we explored the feasibility of applying multispectral high spatial resolution ALOS imagery for fractional cover extraction of rocky outcrops. We selected the dimidiate pixel model (DPM), which has been applied in previous studies, and spectral mixture analysis (SMA; including simple endmember spectral mixture analysis (SESMA) and multiple endmember spectral mixture analysis (MESMA)) to explore the feasibility of using remote images for KRD monitoring and improve accuracy for estimating fractions. Results from MESMA achieved high overall accuracy (76.4%) in monitoring percentage of rocky outcrop fraction in the study area. SESMA appears to underestimate percentage of rocky outcrop likely because the development of KRD was driven by complex factors (soil erosion, dissolution and anthropogenic disturbances). This results in spectral reflectance of rocky outcrop being variable in different settings. Predicted exposed bedrock coverage using SESMA and MESMA was similar in sun-lit and shaded areas although predictions from SESMA were smaller than reference data. DPM underestimated the fractional cover of rocky outcrops on south-facing slopes and overestimated it in shaded areas. Furthermore, SESMA and MESMA effectively reduced topographic effects. We conclude that it is better to extract percentage of rocky outcrop using MESMA in the karst region of southwestern China. Remote sensing is emerging as a feasible method to extract surface condition information in heterogeneous and rugged landscapes.