Groundwater plays a crucial role in maintaining baseflow in rivers and ensuring water supply, particularly in alpine regions where the freeze–thaw (FT) cycle exerts a strong influence. However, a systematic understanding is still lacking regarding how FT processes affect the composition of groundwater recharge sources and the transitions among recharge pathways. This study takes the Qinghai Lake basin (QLB) as a case example and combines water isotope and hydrometeorological data to quantify the dynamic characteristics of groundwater recharge sources and pathways during the FT periods. The study found that soil water (57.0 %–76.3 %) is not only the main recharge source for groundwater during the FT periods but also serves as a key transitional reservoir linking rainfall 13.8 %–26.1 %) and snowmelt (7.9 %–22.0 %) to groundwater recharge. The thawing process enhances the vertical connectivity of the soil profile, facilitating the recharge of groundwater from snowmelt and the 60–90 cm soil layer. Furthermore, the lc–excess value of groundwater gradually shifts from values closer to soil water to those closer to precipitation, indicating that piston flow gradually weakens during the process of groundwater recharge by soil water, while preferential flow intensifies, resulting in a pattern where piston flow and preferential flow coexist. Spatially, in the middle and upper regions dominated by permafrost, groundwater is primarily recharged by water from the 0–60 cm soil layer traveling along longer hydrological pathways, whereas in the downstream regions of the basin dominated by seasonal frozen ground, groundwater is primarily recharged by rapid infiltration from the 30–90 cm soil layer. Our research demonstrates that in alpine permafrost regions, freeze-thaw processes regulate water storage and transport, thereby further influencing the recharge sources and pathways of shallow groundwater.