Global climate change poses a significant threat to vulnerable island ecosystems, jeopardizing biodiversity and habitats, and potentially leading to species extinction. The paleoenvironmental history of St. Paul Island (Bering Sea), the last refuge for woolly mammoths (Mammuthus primigenius), exemplifies this threat during the 6–4 kyr BP interval. Existing research posits that, unlike mainland extinction attributed to hunting, St. Paul mammoths likely perished during the mid-Holocene due to climate-driven habitat loss, resulting in food scarcity and critical freshwater depletion. This crucial qualitative inference demands robust, direct quantitative evidence from paleoclimatic proxies. To address this need, we compiled and analyzed palynological records from over 20 sediment cores collected from St. Paul Island and the adjacent Bering Sea coastal mainland. Utilizing the Modern Analogue Technique (MAT), we reconstructed the island's biome evolution and quantitatively derived monthly (January and July) and annual precipitation throughout the Holocene. Focusing on 6–4 kyr BP, we performed a quantitative reconstruction of spatiotemporal precipitation patterns across the Bering Sea region, mapping annual precipitation isolines for five key time slices: 6, 5.5, 5, 4.5, and 4 kyr BP. Results show that before 6.6 kyr BP, the island had high annual precipitation (~600 mm/yr) and a biome oscillating between shrub tundra and cold coniferous forest, sustaining a stable relict mammoth population. However, between 6.6 and 4.1 kyr BP, precipitation consistently declined to 400~450 mm/yr, forcing the biome to transition into an arid, desert-like type. This desiccation directly induced critical food and freshwater stress that led to the extinction of the mammoths. Furthermore, annual precipitation along the western Bering Sea coastal regions plummeted to ~240 mm by 4 kyr BP. This quantitative reconstruction provides more direct paleoclimatic evidence (precipitation decline) that supports the freshwater depletion hypothesis, offering a climatic mechanism to supplement the sea-level rise driver.