Climate and landscape changes since the late Holocene have received increasing attention. The Altai region, which is located at the intersection of the Inner Asian Mountain Corridor and the Eurasian Steppe Roads, is relatively poorly studied. In this study, based on robust radiocarbon ages and detailed pollen analyses, the history of climate and landscape changes was reconstructed from Yileimu Lake, southern Altai Mountains during the past 3500 years. Four stages of vegetation change are identified: (1) During 1550 BCE–720 BCE, the vegetation was taiga (mainly Picea and Betula) in uplands, and steppe (dominated by Artemisia, Poaceae and Cyperaceae) around the lake, indicating a humid climate, which was favorable for the expansion of human activities including enhanced nomadic pastoralism in Altai Mountains and transcontinental culture exchange along the proto‐Silk Roads. (2) During 720 BCE–390 CE, there was a stepwise decrease in Picea, rapid increase and then decrease in Betula, and gradual increases in contents of Poaceae and Thalictrum pollen, and fern spores, indicating a warm and moderately humid climate, with evidence of more intense human activities during 20 BCE–390 CE. (3) During 390 CE–1560 CE, desert-steppe (with high Amaranthaceae, Caryophyllaceae, Ephedra and Cyperaceae content) developed in response to an increasing arid climate and/or enhanced human activities. (4) After 1560 CE, taiga and steppe recovered due to the humid climate. Human activities have become the key factor affecting vegetation since the past 2000 years. In addition, the vegetation response to an Ms ≥ 8.0 earthquake that occurred around 1550 BCE was characterized by a rapid recovery of Betula, followed by Artemisia and Picea. Restoration of vegetation helps to reduce soil erosion and afforest exposed landslides.