The plate tectonic history of the hypothesized ‘proto-South China Sea’ (PSCS) ocean basin and surrounding SE Asia since Cenozoic times is controversial. We implement four diverse PSCS plate reconstructions into global geodynamic models to constrain PSCS plate tectonics and possible slab locations. We consider: southward versus double-sided PSCS subduction models; earlier (Eocene) or later (late Oligocene) initiation of Borneo counterclockwise rotations; and, larger or smaller reconstructed Philippine Sea plate sizes. We compare our modeling results against tomographic images by taking into account mineralogical effects and the finite resolution of seismic tomography. All geodynamic models reproduce the tomographically-imaged Sunda slabs beneath Peninsular Malaysia, Sumatra and Java. Southward PSCS subduction produces slabs beneath present Palawan, northern Borneo, and offshore Palawan. Double-sided PSCS subduction combined with earlier Borneo rotations uniquely reproduces sub-horizontal slabs under the southern South China Sea (SCS) at ~400 to 700 km depths; these models best fit seismic tomography. A smaller Philippine Sea (PS) plate with a ~1000 km-long restored Ryukyu slab was superior to a very large PS plate. Taken together, the four end-member plate models predict PSCS slabs at <900 km depths under present-day Borneo, the SCS, the Sulu and Celebes seas, and the southern Philippines. Regardless of plate models, we predicted passive mantle upwellings under Indochina during late Eocene-Oligocene times, and downwellings under the SCS during the late Cenozoic that do not support a deep-origin ‘Hainan plume’. Modeled Sundaland dynamic topography depends strongly on the imposed plate model, varying by several hundred meters.