Wind erosion is one of the most widespread and severe natural hazards in arid, semiarid, and semihumid regions worldwide. The Three-North region (TNR) (Northeast China, North China, and Northwest China) of China includes 90% of the wind erosion area in China. In response to the harsh environmental conditions in the TNR, China initiated a series of ecological programs, including the Three-North Afforestation Program and Grain for Green. However, little is known about the effect of these ecological programs on wind erosion. Therefore, within our study, we estimated the spatiotemporal variations in wind erosion in the TNR between 1981–2020 with a revised wind erosion model and analyzed its driving mechanism. Then, the ecological programs’ effects on wind erosion changes was identified. The results showed the following. (1) From 1981 to 2020, wind erosion showed a clear downward trend of 99.02 t km−2 a−1, with a slope. On average, the areas of mild, moderate, severe, more severe, and very severe wind erosion accounted for 28.76%, 7.17%, 3.92%, 3.72%, and 13.29% of the total in the TNR, respectively. (2) Wind erosion variation was inconsistent in different parts of the TNR. The wind erosion expressed a long-term decreasing trend in Northeast China and the Loess Plateau, a nonsignificant change in North Central China, and an increasing trend in Northwest China. (3) On average, ecological programs were very limited in reducing erosion at the regional scale, with a contribution of approximately 5.93% in the TNR because of the relatively small scope of ecological programs’ implementation. Climate change played a key role in adjusting wind erosion; wind speed, temperature, and precipitation affected 57.58% of the TNR. Human interference (proportion of cropland and grassland areas in a 1 km ×1 km grid) affected 8.78% of the TNR. Thus, the persistent complement of ecological programs, reasonable human activities, and timely observation is a method to alleviate wind erosion in the TNR.