Through a comprehensive study of magnetostratigraphy and sedimentology of several basins in the northeastern Tibetan Plateau, we reveal that the study area mainly experienced six tectonic uplift stages at approximately 52 Ma, 34–30 Ma, 24–20 Ma, 16–12 Ma, 8–6 Ma, and 3.6–2.6 Ma. Comprehensive analyses of pollen assemblages from the Qaidam, Linxia, Xining, and West Jiuquan Basins show that the northeastern Tibetan Plateau has undergone six major changes in vegetation types and climate: 50–40 Ma for the warm-humid forest vegetation, 40–23 Ma for the warm-arid and temperate-arid forest steppe vegetation, 23–18.6 Ma for the warm-humid and temperate-humid forest vegetation, 18.6–8.5 Ma for the warm-humid and cool-humid forest steppe vegetation, 8.6–5 Ma for the temperate sub-humid savanna steppe vegetation, and 5–1.8 Ma for the cold-arid steppe vegetation. Comprehensive comparisons of tectonic uplift events inferred from sedimentary records, climatic changes inferred from pollen, and global climate changes show that in the northeastern Tibetan Plateau the climate in the Paleogene at low altitude was mainly controlled by the global climate change, while that in the Neogene interval with high altitude landscapes of mountains and basins is more controlled by altitude and morphology.