Atmospheric dust plays a critical role in Earth's climate system and marine biogeochemistry, but how dust varied during the Phanerozoic is still unclear. Here, we simulate the global dust cycle and its climatic impacts during the whole Phanerozoic using an Earth system model with interactive dust. Our results show that the colonization of land by plants near the end of the Silurian caused a fundamental reorganization of the global dust emission, driving a transition from an uninhibited, highly intense dust cycle to one limited largely to unvegetated subtropical regions. Since 410 Ma, subtropical land area and continental fragmentation have acted as the primary controls on dust emissions. Crucially, while total ocean dust deposition broadly follows global emission trends, the oceanic fraction of dust deposition is strongly regulated by paleogeography; more fragmented continental configurations allow dust to be transported more efficiently to the ocean. By comparing the result of dynamically active dust experiments against that of globally uniform prescribed dust experiments, we explicitly isolate the spatiotemporally heterogeneous radiative forcing induced by interactive dust cycles. The uniform dust assumption misrepresents land surface climate, underestimating dust-induced cooling during vegetation-free intervals but overestimating it after plant colonization. Although the first-order temperature response is driven by shortwave radiative attenuation, the final regional response is strongly modulated by localized feedbacks, including snow–albedo, adjustments of cloud and ocean circulation. Overall, this study underscores that deep-time dust is not merely a passive aerosol tracer but an active component of the coupled Earth system that tightly links paleogeography, terrestrial vegetation, marine biogeochemistry, and climate evolution. The modelled dust distribution compares well with the geological records in general but systematically underestimating the dust emission region since 100 Ma, probably because of the overestimation of vegetation by the model when the fragmentation of continents is high. The present-day dust emission and atmospheric dust loading may be the highest over the past 200 Ma, mainly due to its large subtropical land area.