The present study has focused on the environmental changes and evidences for sedimentation in the Lake Khuvsgul catchment during the Holocene period, inferred from short core sediment (BO03) from the eastern shore of Borsog Bay, which were analyzed in order to review records of the Holocene climatic evolution and Holocene history in Northern Mongolia. For the purpose of reconstruction of natural phenomenon that occurred in the lake catchment system during the Holocene, physical and chemical properties including HCl-soluble material, biogenic silica, organic matter and grain size distribution of minerals in the core sediments have been analyzed in this study. The vertical variations in composition for these properties show distinctly that five lines of paleoenvironmental evidence occurred in the lake catchment during the Holocene. A modified age model resulting from AMS carbon dating for the BO03 core sediment shows timings of these environmental events at 9.5 Kyr BP, 8.0 Kyr BP, 5.6 Kyr BP and 3.2 Kyr BP, respectively. Paleoenvironmental changes in the Lake Khuvsgul catchment system during the Holocene highlight distinctive features of the hydrological regime and geomorphologic evolution in the lake catchment due to regional landscape and global climatic changes corresponding with the Holocene optimum and thermal optimum. In particular, the change of hydrologic regime based on the sedimentological evidence has been caused by not only overland flow due to melting water, but also base flow due to thick permafrost around Khuvsgul region.