The Mindanao Current (MC), a dominant tropical Pacific western boundary current, fuels the Indonesian Throughflow (ITF), the only Pacific-Indian interoceanic conduit in the tropics, with both systems featuring subsurface velocity maxima (SVMs). Reanalysis and high-resolution model data reveal divergent trends over the past 30 years: MC’s SVM weakened and deepened, whereas ITF’s SVM intensified and shoaled. These trends stem from the negative wind stress curl over the northwestern Pacific, which forces a southward shift  North Equatorial Current (NEC) bifurcation and a weakening of the Mindanao Dome. The deepening and weakening of MC SVM reduce equatorward surface heat transport from off-equatorial Pacific, while a shallower and intensified ITF SVM enhances surface heat transport, increasing warm surface waters into the Indian Ocean. Under future global warming, the iHESP projections suggest the MC’s SVM will reverse to stronger and shallower, affecting heat and freshwater exchanges between the Pacific and Indian Oceans.