In the face of climate change and human activities, Central Asia’s (CA) terminal lake basins (TLBs) are shrinking, leading to deteriorating natural environments and serious soil wind erosion (SWE), which threatens regional socio-economic development, human health, and safety. Limited research on SWE and population exposure risk (PER) in these areas prompted this study, which applied the RWEQ and a PER model to assess the spatiotemporal changes in SWE and PER in TLBs in CA, including the Ili River Basin (IRB), Tarim River Basin (TRB), Syr Darya River Basin (SRB), and Amu Darya River Basin (ARB), from 2000 to 2020. We analyzed the driving factors of SWE and used the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model to simulate dust event trajectories. The findings from 2000 to 2020 show a spatial reduction trend in SWE and PER, with primary SWE areas in the Taklamakan Desert, Aral Sea Basin, and Lake Balkhash. Significant PER was observed along the Tarim River, near Lake Balkhash, and in the middle and lower reaches of the ARB and SRB. Over the past 21 years, temporal trends in SWE have occurred across basins, decreasing in the IRB, but increasing in the TRB, SRB, and ARB. Dust movement trajectories indicate that dust from the lower reaches of the SRB and ARB could affect Europe, while dust from the TRB could impact northern China and Japan. Correlations between SWE, NDVI, temperature, and precipitation revealed a negative correlation between precipitation and NDVI, suggesting an inhibitory impact of precipitation and vegetation cover on SWE. SWE also varied significantly under different LUCCs, with increases in cropland, forestland, and desert land, and decreases in grassland and wetland. These insights are vital for understanding SWE and PER in TLBs and offer theoretical support for emergency mitigation in arid regions.