Land desertification is a bad manifestation of environmental degradation, which is jointly affected by irrational economic activities and fragile ecological environment. The red soil region in southern China is one of the most serious areas of soil and water loss. Soil and water loss has resulted in the decline of the soil and water conservation function, and the intensification of land desertification, thereby introducing huge ecological risks to the red soil region. In this study, the Dongjiang source area (DSA), a typical red soil region in South China, was selected as the study area. The random forest (RF) algorithm was used to extract refined desertification information, including spectrum, texture, and topography information, from the features of the DSA. The spatiotemporal evolution pattern and disturbance factors of desertification in the DSA from 1986 to 2020 was subsequently analyzed. Furthermore, to understand desertification development in a more detailed perspective, the land desertification changes in 2020 were revealed from the sub-watershed scale, and the spatiotemporal difference of a typical sub-watershed were deeply analyzed. The results indicate that the time period can be divided into three stages of desertification, namely development (1990–2000), stable reversal (2010–2015), and rapid reversal (2015–2020). The main reasons for the rapid reversal of desertification in this area are the strict ecological restoration policy and orchard environmental management measures implemented in southern Jiangxi during 2015–2020; however, the desertification in the DSA has not recovered to the pre-disturbed level. Moreover, it was found that the spatial distribution of the desertified land is basically consistent with the direction of the rivers in the DSA; with the main rivers as the center, the desertified land expands outwards in a flaky shape, and exhibits strong regionality. The spatial distributions of the desertified land in 2020 were found to be significantly different among the 18 sub-watersheds in the DSA, and the areas with larger differences were found to be concentrated in Dingnan County, which is mainly related to orchard reclamation. The desertification in the upper and lower reaches of the Xunwu river sub-watershed is continuously affected by the development of orchards and cultivated land on both sides of the river, and the desertification disturbance in the middle reaches is mainly caused by rare-earth element (REE) mining; the regional spatial distribution above the severely desertified land (SDL) grade is consistent with the concentrated area of REE minerals, which indicates that REE mining is an important reason for the aggravation of the desertification in the DSA.