Wind erosion is the main form of soil erosion in arid and semi-arid areas. It leads to soil loss and land degradation, which aggravates ecosystem vulnerability and threatens regional sustainable development. The assessment of wind erosion and the study of its driving factors can reduce soil wind erosion and provide decision-making assistance to solve environmental problems. Southern Africa is affected by severe soil erosion, which has brought a series of development problems, such as food crises and poverty. This study used meteorological and remote sensing data, and the revised wind erosion equation model to explore the temporal and spatial dynamics of soil erosion in southern Africa from 1991 to 2015. The impact of climate dynamics on soil wind erosion was also analyzed. The results showed that wind erosion fluctuated during the study period, and it first showed a downward trend and then stabilized at a relatively low level after 2010. Soil wind erosion across 66.65% of the study area significantly decreased (p < 0.05) and near-surface wind speed was the most important factor. The change in wind speed had a positive impact on soil wind erosion across 68.18% of the area. Temperature and precipitation were significantly related to soil wind erosion over 18.96% and 24.63% of the area, respectively. Both can also indirectly affect soil wind erosion through their effects on vegetation cover. This study will help decision-makers to evaluate areas that are at high-risk from soil erosion in southern Africa and enable them to effectively protect fragile ecosystems.