Climatic instability has major impacts on water resources and catastrophic effects on fragile ecosystems in arid Central Asia (ACA). Short-term (decadal to centennial) climate fluctuations over the last millennium can help predict whether future climate instability and the frequency of extreme climate events will increase. Research has revealed higher moisture variability during the Little Ice Age (LIA) than during the Medieval Warm Period (MWP). However, the age control quality and temporal resolution of the proxy records that are used make it difficult to characterize the specific unstable climate fluctuations on decadal to centennial scales. Here, we present a well‐dated high‐resolution ostracod record from a remote alpine lake (Dalongchi Lake) in the central Tianshan Mountains, northwestern China, ACA, which has an average ∼ 3–4-year resolution and provides a record of inferred lake level fluctuations over the past millennium. The abundance of deep-water adapted Fabaeformiscandona gyirongensis was generally higher in the LIA and lower in the MWP and Current Warm Period (CWP), which confirmed the associations of warm–dry and cold–wet conditions in ACA. Notably, our ostracod records captured several distinct and dramatic secondary lake level fluctuations during the LIA. The abundance of F. gyirongensis peaked in four intervals at 1380–1460, 1540–1580, 1640–1720 and 1800–1940 CE, indicating sharp lake level increases, while the abundance decreased sharply in the three intervals of 1460–1540, 1580–1640 and 1720–1800 CE, indicating significant lake level decreases. There was a strong, inverse relationship between the lake level and the total solar irradiance (TSI) on the multidecadal to centennial scale, and the spectral analysis and wavelet coherence results suggest the presence of Gleissberg cycles. We propose that the century Gleissberg solar cycle directly affected regional humidity changes through temperature and evaporation forcing. Our findings suggest that solar activity probably plays an important role in determining future hydroclimatic changes in ACA.