Modern observations have presented linkages between subsurface waters of the western Pacific warm pool and both El Niño/Southern Oscillation-related and extratropic-controlled upper-ocean stratification on interannual timescales. Moreover, studies have showed that such controls may operate on orbital cycles, although the details remain unclear. Here we present paired temperature and salinity reconstructions for the surface and thermocline waters in the central western Pacific warm pool over the past 360,000 years, as well as transit modeling results from an Earth system model. Our results show that variations in subsurface temperature and salinity in the western Pacific warm pool have consistently correlated with the shallow meridional overturning cell over the past four glacial-interglacial cycles, and they vary on eccentricity and precession cycles. The shallow meridional over- turning cell regulates subsurface waters of the western Pacific warm pool by changing subtropical surface water density and thus equatorial upper-ocean stratification, acting as an El Niño/Southern Oscillation-like process in the precession band. Therefore, the western Pacific warm pool is critical in connecting the austral shallow meridional overturning cell to the Earth’s climate system on orbital timescales.