The prolonged convergence along the Southeast Asian margin from the Mesozoic to Cenozoic shaped the region into a complex tectonic collage of microblocks of diverse origin and evolutionary history. Among these microblocks, the formation and paleogeographic evolution of the Palawan continental terrane remain issues of uncertainty and controversy, especially regarding the petrogenesis of the oldest rocks and the conjugate relationship with the South China margin. This study examined these issues from the perspective of detrital fingerprints (including geochemistry, heavy mineral, and zircon U-Pb geochronology) of Mesozoic to Cenozoic strata from Palawan Island and basins of the northern South China Sea. The across-margin comparison of provenance signatures, favored by a comprehensive data compilation and a revision of the stratigraphic framework using the youngest zircon ages, provides insights into regional paleogeographic reconstructions from the Jurassic to the Miocene. The results reveal provenance shifts that correspond to the paleogeography of the Palawan continental terrane evolving from an accretionary complex in the Jurassic to a rifted margin in the early Cenozoic and finally to a microcontinent in the middle Cenozoic. Based on comparable provenance signatures, the terrane is interpreted to have been conjugated to the northeastern South China Sea margin from the Mesozoic until the Oligocene spreading of the South China Sea. The terrane likely existed as a northern passive margin of the proto–South China Sea from the latest Cretaceous to early Cenozoic before the oceanic crust of the latter was emplaced over the former during the Oligocene–Miocene.