Interactions among late Cenozoic global cooling, tectonic activity and regional climate evolution of the northeastern Tibetan Plateau remain elusive. To further understand the relative contributions of global climate change and tectonism, we conducted a comprehensive study of heavy minerals, rock magnetism, and branched glycerol dialkyl glycerol tetraethers (brGDGTs) in late Cenozoic sediments of the Laojunmiao section (ca. 12.7 Ma to 5 Ma) in the Jiuxi Basin. Our results reveal a notable increase in magnetic susceptibility (χ) and saturation isothermal remanent magnetization (SIRM) at 8.5 Ma, aligning with an accelerated decrease in temperature captured by brGDGTs. Combined with heavy mineral analysis, we propose that the profound changes in magnetic parameters and temperature are closely linked to the intensive uplift of the northern Qilian Shan since 8.5 Ma. Furthermore, this ongoing uplift has occurred simultaneously with persistent aridification in the Jiuxi Basin and its adjacent regions. The Qilian Shan might have reached a threshold elevation and began to act as a moisture barrier to northwestward moisture since 8.5 Ma. By synthesizing hydroclimate evolution records from the northeastern Tibetan Plateau, we deduce that changing topography resulting from tectonic uplift may have exerted a significant influence on regulating the moisture distribution in this region during the mid- to late Miocene.