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To study the Cenozoic tectonic and paleoenvironmental evolution of northwestern China, we drilled two deep boreholes, JLT1 and JLT2, in the Jartai Basin. Magnetostratigraphy, stratigraphy studies were conducted to establish a chronological framework. Sedimentary facies were reconstructed using lithology, geophysical logs (gamma ray (GR) and resistivity (R)) and measurements of grain size, sediment color (L*, a* and b*) and magnetic susceptibility and its frequency dependence. The stratigraphic sequence of borehole JLT2 is similar to that of Paleogene sediments in basins along the northeastern Tibetan Plateau, which may be the result of the far-field effect of the uplift of the Tibetan Plateau during the Paleocene, via faulting activity. The results of borehole JLT1 indicate that the basin was occupied by alternating desert, lacustrine and alluvial fan environments since ca. 6.7 Ma. During ca. 6.7-3.6 Ma, alternations of aeolian sand and lacustrine facies may reflect climatic cooling and drying, and at that time the area may have been an important sediment source for the aeolian Red Clay of the Loess Plateau. During ca. 3.6-2.1 Ma, alluvial fan development also reflected the uplift of the northeastern Tibetan Plateau, and the area acted as a source region for dust supplied to the Loess Plateau and the Shanxi Graben. The alternations of aeolian sand and lacustrine deposits since ca. 2.1 Ma may have resulted from glacial-interglacial variations of the East Asian Monsoon. Since ca. 1.7 Ma, lacustrine deposition developed, because of the enormous discharge of the Yellow River into the Jartai Basin. A tectonic movement at ca. 0.8 Ma is reflected by lacustrine red clay at the top of borehole JLT1. After the mid-Pleistocene transition, the modern landscape of the Jartai Basin and its adjacent regions were formed.