Solar irradiance changes are thought to play an important role in natural climate variability. How the hydrological conditions were affected by solar irradiance in westerly-controlled arid central Asia (ACA) on decadal/centennial timescales remains poorly understood because of the lack of high-quality records. Here, we integrate 1.2-year-resolution x-ray fluorescence (XRF) scanner-derived carbonate accumulation estimates with 6-year-resolution biomarker and magnetic records in a well-preserved shoreline core from Lake Manas, northwestern China, to reconstruct lake level fluctuations and potential solar imprints over the last millennium. Besides the generally confirmed cool-wet/warm-dry climate pattern in ACA, our data also consistently show frequent and substantial lake level fluctuations, resembling solar activity changes, especially during the ‘Little Ice Age’. Wavelet spectral analyses of our XRF data indicate strong 8- to 16-year, 64- to 128-year and 128- to 256-year cycles, coinciding with the ~11-year Schwabe cycle, ~70- to 100-year Gleissberg cycle, and the ~200-year Suess-de Vries cycle. We therefore suggest the existence of solar imprints on effective moisture fluctuations in ACA over the last millennium, and the potential occurrence of the Schwabe cycle even during the solar minima.