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The Taklimakan Desert in western China contains the second largest shifting sand desert on earth. The onset of this desert formation has been debated between the Eocene, early Miocene, late Miocene, or Pliocene, with each hypothesis having profound implications for the climatic and tectonic evolution of this region. We provide stratigraphic evidence for desert formation based on a new 3800-m-thick stratigraphic section in the northwestern Tarim Basin. Magnetostratigraphy defines 50 magnetozones and constrains the age of these strata to between ca. 15.1 and 1.5 Ma. Fluvial and lacustrine strata at the base of the section change abruptly to eolian sandstone (similar to 1100 m thick) at 12.2 Ma and persist until 7.0 Ma, implying development of an erg system that represents the ancestral Taklimakan Desert. The appearance of sand dunes at 12.2 Ma has no global climate parallel, and resulted from aridification in the rain-shadow behind a growing Tian Shan and Pamir that isolated the Tarim Basin.