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This study aims to reveal Holocene environmental changes on the bases of the physical and chemical analyses of the sediment core obtained from Lake Khuvsgul in Mongolian Plateau and Lake Siling-co in Tibetan Plateau.Analytical results of the Holocene sedimentary sequence in Borsog Bay of Lake Khuvsgul shows that certain environmental shifts at about Little Ice Age and 3.5 ka BP; noticeable increases are detected in mineral grain size, whole grain size, mineral content and grain density during the periods when the organic matter content, biogenic silica content and diatom abundance decreased.Bottom sediment in Lake Siling-co indicates a comparatively large fluctuations in hydrological conditions at a water inflow for a short period at about 3000~4000 a BP; and decreases in the water level at about 4000 a BP and 3500 a BP, when mineral fractions and whole sediments return to coarse grains, mineral content increased, and organic matter and biogenic silica decreased.Analytical results suggest the comparatively large hydrological changes in the inner Asia during the Late Holocene with a similar pattern of the humidity and aridity in the both lakes.