The production, transport, and deposition of mineral dust exert major influences on climate change and Earth’s biogeochemical cycles. Furthermore, their imprint, as recorded in pelagic sediments, provides an avenue for determining past changes in terrestrial aridity and atmospheric circulation patterns in response to global climate change. Here, by examining geochemical and magnetic data obtained from a ferromanganese crust in the western Pacific Ocean, we investigate the eolian dust source-region conditions and dust transport mechanisms from the Asian interior to the Pacific Ocean since the Pliocene. We identify a gradual provenance change in the dust source regions, from a dominant Gobi Desert source during the early Pliocene to a mixed Gobi-Taklimakan Desert source during the late Pliocene and Pleistocene, alongside increasing chemical weathering in those source areas. Climate model simulations suggest that these changes were related to an equatorward shift of the westerly jet and humidification of Central Asia during the gradual transition from a warm Pliocene climate to the cool Pleistocene.