Lower crusts of oceanic plateaus have been rarely studied and their nature remains unclear, due to low probability in preservation. Here we demonstrate that cumulates of the Pengco Complex in central Tibet represent the lower crust of an oceanic plateau generated at ~188 Ma. Mineral crystallization order and geochemistry support their formation via low‐P fractionation from anhydrous basaltic melts. The Pengco cumulates are more magnesium rich and more depleted in rare earth elements than the mid‐ocean ridge cumulates, supporting a mantle source more refractory than the depleted MORB mantle (DMM). However, the extrusive rocks outcropped in the Pengco Complex are younger (161–166 Ma) and have a subducted‐related genesis. Such a temporal and genetical decoupling between the lower and upper crustal rocks in the Pengco Complex resulted from the subduction re‐initiation that was triggered by the oceanic plateau‐continent collision at ~164 Ma.