In the context of climate warming and intensified extreme climate events, the hydrological cycle and processes are increasingly affected, leading to certain spatial and temporal changes in hydrological elements. The pan-Arctic region is one of the most concentrated areas of lake distribution in both count and area on the Earth, and the lakes in this region are very sensitive to climate change. It is essential to understand the characteristics of recent hydrological changes of these lakes. In this study, the water level data for a total of 36 pan-Arctic large lakes (>500 km²) were collected over the past 20 years based on remote sensing or station observations, and their spatio-temporal variation characteristics were analyzed. We used a linear regression model to estimate the changing trend of lake water level, then used the Pearson correlation to analyze its main hydrological variables and atmospheric circulation factors. The Mann-Kendall mutation test was applied to explore the possible reasons for the abrupt changes in lake water level. The results indicated that the water levels of the pan-Arctic lakes showed different degrees of increase overall (mean rate at 0.013 m/a), with 23 lakes (64%) showing an increase in water levels. Only 10 lakes were featured by the linear trends at the 90% statistical significance. Lake Tengiz in Kazakhstan ranked the fastest among these rising lakes, with a change rate of 0.078 m/a. The changes in water level of these pan-Arctic lakes were mainly related to runoff variations, with 19 lakes (53%) showing correlations with increases in runoff. In comparison, increased water levels of the lakes located in Asia were significantly correlated with decreased evaporation, especially Lake Khovsgol. The pan-Arctic lake level changes were mainly associated with El Nino Southern Oscillation, followed by Arctic Oscillation and North Atlantic Oscillation. This study is expected to deepen our scientific understanding on the water level variation patterns and climate impact on the pan-Arctic lakes over the last 20 years.