Alpine regions’ groundwater is crucial to the worldwide hydrological cycle. However, due to the harsh environmental conditions, the distribution and evolution characteristics await clarification. The study area was selected to be the Nagqu River Basin in the Nu-Salween River’s source region. In 2019-2021, we gathered 88,000 monitoring data from nine observation wells and examined the spatiotemporal groundwater table changes in various permafrost zones and freeze-thaw cycles. During the freezing period, entirely frozen period, thawing period, and entirely thawed period, the groundwater table change rates in the permafrost zone were 2.14, 1.54, 1.55, and 2.01 times larger than in the seasonal frost zone, and fluctuation amplitudes were 1.97, 1.28, 1.01 and 1.31 times larger. The average groundwater table change rate and fluctuation amplitude were greatest during the entirely thawed period and lowest during the thawing period, with the maximum change rate reaching 3.64 cm/d during the entirely thawed period of 2019-2020 in the permafrost zone and the minimum change rate of 0.12 cm/d during the thawing period of 2019-2020 in the seasonal frost zone.