Desert dust plays a crucial role in the climate system; while it is relatively well studied for the present day, we still lack knowledge on how it was in the past and on its underlying mechanism in the multi-million-year timescale of Earth’s history. For the first time, we simulate dust emissions using the newly developed DUSTY1.0 model over the past 540 million years with a temporal resolution of ~5 million years. We find that palaeogeography is the primary control of these variations.