•Explored permafrost temperature time–frequency traits in four alpine grasslands.•Alpine meadows were more climate-sensitive than the other three alpine grasslands.•Precipitation and wind speed had significant effects on permafrost.•The varying impacts of vegetation and a sand layer on permafrost were discussed. Permafrost temperature is a vital indicator of climate and permafrost changes, benefiting ecosystem development and informing local climate strategies. Alpine grasslands impact moisture and heat exchange between the surface and atmosphere, thereby affecting the thermal state of underlying permafrost. This study analyzed permafrost temperatures (2004–2019) from various alpine grasslands (including alpine meadow, alpine steppe, alpine desert grassland, and barren land) in the Beiluhe region of the Tibetan Plateau and revealed their connections to climate change and controlling factors, using time–frequency analysis. The findings revealed that in the time–frequency domain, permafrost temperatures exhibited multiple time scales characteristics, driven by climate fluctuations. Changes in the active layer closely followed monthly climate variations, while permafrost dynamics responded to annual climate changes. Significant oscillations with periods of 10–11, 8–9, and 14 years were observed in the surface, permafrost table, and deep permafrost layers, respectively. Among the different types of alpine grasslands, alpine meadows proved to be the most sensitive to climate change, with the intensity of periodic fluctuations initially decreasing and then increasing with depth in alpine meadows, while it consistently decreased with depth in the other three alpine grasslands. The impact of air temperature, precipitation, and wind speed on permafrost dynamics exhibited depth-dependent variations in the time–frequency domain, contrasting with the time domain where permafrost temperature changes were predominantly associated with air temperature across all depths.