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The permafrost response to variations in Arctic vegetation remains controversial. We investigated the consequences of Arctic vegetation greenness variation over the past three decades using a coupled land-atmosphere model and found that it induces air temperature perturbation, which is further amplified by snow cover variation and eventually leaves a footprint on soil temperature. Compared to the atmospheric impacts of vegetation, local shading of vegetation canopy has relatively minor effects on soil temperature. Significant soil warming was observed along the summer snowline between the Low and High Arctic, indicating the direct impact of snow cover variation led by vegetation changes. In the Low Arctic, the winter snowpack insulates the soil from colder air, resulting in less permafrost. In the High Arctic, snow persists for more than 330 d per year and has a strong protection effect on the permafrost as it insulates soil from warmer summer air and reflects solar radiation.