In the context of global change, rocky desertification in the southwestern mountainous region has intensified to some extent, making it urgent to clarify its evolution patterns and dominant driving factors. In this study, based on MODIS data products, an optimal remote sensing monitoring model for rocky desertification was constructed by integrating the Random Forest algorithm, three-dimensional feature space model, and geographical detectors. Subsequently, the evolution patterns and dominant driving factors of rocky desertification from 2000 to 2023 were analyzed and interpreted. The main conclusions were as follows: (1) KNDVI, Albedo, BSI, and RBI were identified as the optimal indicators for characterizing rocky desertification in the southwestern mountainous region. Among them, the KNDVI-Albedo-BSI feature space model demonstrated the highest practical applicability for monitoring rocky desertification, with an overall accuracy of 88.39% and a Kappa coefficient of 0.8522, especially exhibiting high stability and discrimination capability in mild, moderate, and extreme rocky desertification classes. (2) From 2000 to 2023, rocky desertification in the southwestern mountainous region was primarily characterized by mild and moderate levels, mainly distributed in the central and western parts of Guizhou Province, the border areas between Sichuan Province and Chongqing Municipality, and the southwestern and southeastern regions of Yunnan Province. (3) From 2000 to 2023, rocky desertification in the southwestern mountainous region showed an overall improving trend. Specifically, from 2000 to 2010, the region experienced a general improvement, while from 2010 to 2023, the trend continued with overall improvement but localized deterioration in certain areas. (4) The dominant driving factors of rocky desertification underwent significant changes between 2000 and 2023, shifting from co-dominance by natural factors in 2000, to a strengthened coupling effect of human activities and natural elements in 2010, and finally to precipitation becoming the primary driver in 2023. The findings of this study provided essential data and decision-making support for the comprehensive management and mitigation of rocky desertification in the southwestern mountainous region.