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Lake Hulun is the fifth‐largest lake in China, playing a substantial role in maintaining the balance of the grassland ecosystem of the Mongolia Plateau, which is a crucial ecological barrier in North China. To better understand the changing characteristics of Lake Hulun and the driving mechanisms, it is necessary to investigate the water storage changes of Lake Hulun on extended timescales. The main objective of this study is to reconstruct the water storage time series of Lake Hulun over the past century. We employed a machine learning approach termed the extreme gradient boosting tree (XGBoost) to reconstruct the water storage changes over a one‐century timescale based on the generated bathymetry and satellite altimetry data and investigated the relationships with hydrological and climatic variables in long term. Results show that the water storage changes from 1961 to 2019 were featured by four fluctuation phases, with the highest water storage observed in 1991 (14.02 Gt) and the lowest point in 2012 (5.18 Gt). The century‐scale reconstruction result reveals that the water storage of Lake Hulun reached the highest point in the 1960s within the period of 1910–2019. The lowest stage occurred in the sub‐period of the 1930s–1940s, which was even lower than the alerted shrinkage stage in 2012. The predictive model results indicate the effective performance of the XGBoost model in reconstructing century‐scale water storage variations, with the mean absolute error of 0.68, normalized root mean square error of 0.11, Nash–Sutcliffe efficiency of 0.97, and correlation coefficient of 0.94. The annual fluctuations of water storage were mostly affected by precipitation, followed by vapor pressure, temperature, potential evapotranspiration, and wet day frequency. The dominating characteristics of different variables vary evidently with different sub‐periods. The atmospheric circulations of the Arctic Oscillation, El Nino Southern Oscillation, Pacific Decadal Oscillation, and North Atlantic Oscillation have tight associations with the water storage variations of Lake Hulun, which change with different study periods. Plain Language Sumamry: To better understand the changing characteristics of Lake Hulun and the driving mechanisms, it is necessary to investigate the water storage changes of Lake Hulun on extended timescales (e.g., century timescale). The main objective of this study is to reconstruct the water storage time series of Lake Hulun over the past one century. We employed a machine learning approach termed the extreme gradient boosting tree (XGBoost) to reconstruct the one‐century water storage changes and investigated the relationships with hydrological and climatic variables in long term. The century‐scale reconstruction result reveals that the water storage reached the highest point in the 1960s within the period 1910‐2019. The lowest stage occurred in the 1930s‐1940s, which was even lower than the alarted shrinkage stage in 2012. The annual fluctuations of water storage were mostly affected by precipitation, followed by vapor pressure, wet day frequency, potential evapotranspiration, and temperature. However, the dominating characteristics of different variables vary evidently with different sub‐periods. This study is expected to provide an efficient technical solution of reconstructing long‐term lake water storage records and to advance our scientific understanding of the characteristics of lake water balances in response to climate change and variability in the Mongolia Plateau. Key Points: The complete bathymetry map of Lake Hulun was constructed based multi‐source remote sensing dataA machine learning approach was employed to reconstruct the century‐scale water storage of Lake HulunThe potential links of one‐century variations of lake water storage with climatic variables and atmospheric circulations [ABSTRACT FROM AUTHOR]