The Junggar Basin, located in mid-latitude Central Asia, is an inland basin that is one of the remotest area from any open seas on Earth. Knowledge about the paleoclimatic change and the relevant driving factors in this specific geographical region is critically important for understanding the Cenozoic aridification processes in the Asian hinterland. In this study, we focused on Miocene strata in the northwestern Junggar Basin, which consist of middle Miocene fluviolacustrine sediments and a late Miocene aeolian/reworked red clay. Our data of the paleoclimatic indices of color index, magnetic susceptibility and stable isotopes indicate a middle Miocene warm humid climate between 17.5 and 14 Ma, and a subsequent shift to an arid climate after 14 Ma. This paleoclimatic shift was synchronous with a biotic turnover marked by a transition from a high degree of mammal diversity dominated by large-sized mammals living in a humid forest grassland during the Middle Miocene Climatic Optimum to a late Miocene small-sized mammal-dominant fauna living in dry open steppe. The above correlations imply an intrinsic link between environmental change and biotic evolution. We suggest that a decrease in sea surface temperature and the westward retreat of Paratethys induced by global cooling were the key factors responsible for the enhanced aridity of the Asian inland after 14 Ma, which controlled the reduced water vapor transported by the Westerlies to the interior of Asia.