The North Pacific subtropical gyre (NPSG) plays a major role in present global ocean circulation. At times, the gyre has coursed through the South China Sea, but its role in the evolutionary development of that Sea remains uncertain. This work systematically describes a major shift in NPSG paleo-circulation evident from sedimentary features observed in seismic and bathymetric data. These data outline two contourite depositional systems—a buried one formed in the late Miocene, and a latest Miocene to present-day system. The two are divided by a prominent regional discontinuity that represents a major shift in paleo-circulation during the latest Miocene (~ 6.5 Ma). The shift coincides with the further restriction of the South China Sea with respect to the North Pacific due to the formation of the Luzon Strait as a consequence of further northwest movement of the Philippine Sea plate. Before that restriction, data indicate vigorous NPSG circulation in the South China Sea. Semi-closure, however, established a new oceanographic circulation regime in the latest Miocene. This work demonstrates the significant role of recent plate tectonics, gateway development, and marginal seas in the establishment of modern global ocean circulation.