Abstract Formation of marginal sea basins is generally considered to be closely linked to mantle flow, but it is still ambiguous due to limited evidence from seismic anisotropy. Here, we investigate three‐dimensional shear‐wave azimuthal anisotropy in the lithosphere beneath the Philippine Sea Plate (PSP) and its surrounding regions. Our results show that the fast velocity directions in the lower lithosphere beneath the South China Sea (SCS) and northern West Philippine Basin (WPB) are roughly perpendicular to their seafloor spreading directions, whereas those in the upper lithosphere of the SCS and southern WPB are subparallel to their seafloor spreading directions. This feature suggests that eastward mantle flow has significantly reshaped the WPB lithospheric mantle after its formation and influenced the SCS lithospheric mantle formation. Our results provide robust seismic evidence that eastward mantle flow has a considerable contribution to the lithosphere formation of the marginal sea basins in and around the PSP.