<p>This study characterizes for the first time the two largest submarine fans surrounding Taiwan, the Penghu Fan and the Gaoping Fan, based on detailed mapping of depositional elements through newly integrated MCS data. These sedimentary bodies, previously unrecognized due to the deformation related to arc–continent convergence, record the major sediment-dispersal systems of western and southern Taiwan. The Penghu Fan is an elongated, fine-grained system with multistage leveed channels, fed by the Penghu Canyon and likely the Choushui River, whereas the Gaoping Fan is a lobate, mixed sand-mud-rich fan fed by the Gaoping Canyon and Gaoping River. Together, they contain an estimated 9000 km³ of sediment, underscoring their significance in regional sediment routing and margin evolution. We identify three tectonosedimentary stages during the passive margin to active margin transition: early pre-growth, late pre-growth, and syn-growth. Key surfaces correlate with onshore stratigraphic records, revealing how the Pleistocene Penghu and Gaoping Canyon–Fan systems developed during passive margin-active margin transition and providing new constraints on the southward propagation of depositional systems and the Taiwan orogeny.</p>