[Objective] The key ecological functional zone (KEFZ) of the Inner Mongolia Autonomous Region serves as a critical ecological barrier for the security of Northern China. The ecosystem type conversion and its impact on soil wind erosion was analysed in order to provide scientific reference for promoting ecological environment security and green development in this region. [Methods] The revised wind erosion equation (RWEQ) model based on land use, meteorology, and basic geographical information data was adopted to determine spatiotemporal changes in ecosystem structure and soil wind erosion in the KEFZ. This method revealed the impacts of ecosystem type changes on soil wind erosion. [Results] ① Substantial conversion between ecosystems in the KEFZ was observed, with a total area of change amounting to 6 019.59 km² from 2000 to 2022. The main transformations were between grasslands and deserts, and between cultivated land and forest-grassland ecosystems. The ecosystem tended to stabilise after 2015, with a reduction in the intensity of changes across various ecosystem types. ② The average soil wind erosion modulus in the KEFZ was 56.39 t/hm², with the erosion levels the highest in desert ecosystems, followed by grasslands, farmlands, and forests. Soil wind erosion was predominantly slight and light, mainly occurring in areas such as the Greater and Lesser Khingan Range forest ecological function area and the Horqin Grassland ecological function area. ③ The conversion between different types of ecosystems in the KEFZ resulted in a net reduction in soil wind erosion of 1.08×10⁸ t. Ecological restoration, land reclamation, grassland quality improvement, desertification control, and the expansion of construction land decreased soil wind erosion modulus by 0.11, 0.23, 0.66, 0.84 t/hm², and 0.68 t/hm², respectively. [Conclusion] Strengthening the consolidation of the effectiveness of ecological management in the KEFZ and avoiding the occurrence of and new land reclamation will be conducive to the comprehensive prevention and control of desertification and high-quality development in Inner Mongolia Autonomous Region.