Abstract: With Honghe Hani and Yi Autonomous Prefecture in Yunnan Province as the study area, we acquired Landsat time-series images from 2000 to 2020 using the Google Earth Engine platform and constructed a rocky desertification severity dataset by calculating fractional vegetation cover and bare rock exposure rate. The temporal evolution and spatial clustering characteristics of the severity distribution were characterized by combining a transition matrix with spatial statistical methods, while the direction and significance of changes were identified using Theil–Sen trend estimation and the Mann–Kendall test. Furthermore, an optimal-parameter Geodetector model was employed to quantify the explanatory power of climate, topography and geology, land-use change, and anthropogenic factors for spatial heterogeneity, thereby revealing the interaction-enhancement effects among key factors. The results indicate that the spatial pattern of rocky desertification is significantly heterogeneous, with rocky desertification-free areas mainly distributed in the northwestern and southeastern parts, areas dominated by moderate rocky desertification in the central, northern, and northeastern parts, and scattered patches of severe and extremely severe rocky desertification. From 2000 to 2020, rocky desertification in Honghe Prefecture exhibited a fluctuating yet overall improving trend, indicating that its expansion had been effectively restrained. The severity grades of rocky desertification displayed stage-specific fluctuations and distinct spatial transitions, with significant spatial differences between areas of improvement and deterioration. Areas exhibiting significant changes were mainly distributed in regions characterized by fragmented terrain, sensitive lithology, and intense anthropogenic activities. Ecological productivity serves as an important process constraint affecting the spatial heterogeneity of rocky desertification. Background factors related to climate and topography primarily act through indirect regulation and environmental constraints. Natural constraints and anthropogenic disturbances jointly influence the spatial heterogeneity of rocky desertification, and the explanatory power of multi-factor interactions is generally higher than that of individual factors.