During the last deglaciation period, climate changes in the northern and southern high-latitude regions show a pattern of so-called “bipolar seesaw” on millennial scale. Previous research interpreted that the weakening of the Atlantic Meridional Overturning Circulation (AMOC) and the associated north-south migration of the Intertropical Convergence Zone (ITCZ) influenced the interhemispheric heat redistribution and thus climate state. However, such a hypothesis lacks the support from the western tropical Pacific, in which the deglacial millennial-scale changes is unclear as the published reconstructions usually conflict with one another. As the major oceanic heat source, the Western Pacific Warm Pool (WPWP) affects the global climate system, with its sea surface temperature (SST) change forcing the tropical atmospheric circulation and its thermocline dynamic modulating the upper-ocean heat content and thermal structure. This study explores the upper-water temperature changes during the transition from the Last Glacial Maximum (LGM) to the Holocene, i.e., the last deglaciation (~23−8 ka). Foraminifera are inferred to calcify in equilibrium with the seawater they live in, make it possible to reconstruct the environmental properties of corresponding water masses where certain foraminifera dwell. We analyzed the δ 18O and Mg/Ca of the mixed-layer dwelling planktonic foraminifera Globigerinoides ruber and the upper-thermocline dweller Pulleniatina obliquiloculata from sediment core MD01-2386 locating at the core of WPWP, and reconstructed decadal-resolved records of SST and thermocline water temperature (TWT) for the last deglaciation. The reconstructed results show that: (1) SST and TWT started initial warming onsets around 20−21 ka, following the initial decrease of precession parameter; (2) SST and TWT stopped warming and plateaued during the interval of Heinrich stadial 1 (HS-1) and Younger Dryas (YD; (3) TWT varied with larger amplitudes than SST. Further, we compared the SST and TWT of core MD01-2386 with the proxy-records of temperature and precipitation of the WPWP and the model-output of El Nino variability. The records of SST, TWT and the planktonic foraminifera δ 18O from the western equatorial Pacific are coherent with the Borneo stalagmite δ 18O, thus suggesting the coupled feedbacks among the thermocline dynamic, sea-surface heating and atmospheric convective activity over the heart of WPWP during the last deglaciation. While, contrasts exist between the records of near-equator region and off-equator area and thus suggests opposite changes in the atmospheric convective activity near the equator and the hydrological cycle change outside the equator. This finding may indicate a relative migration or intensity change of the atmospheric convection center, rather than a north-south shift of the rain belt. In addition, the planktonic foraminiferal proxy records demonstrate significant centennial-scale variabilities, mainly on the periodicity of 220−260 a. This cycle is coherent with the 10Be record of ice core and roughly coincident with the Suess cycle of solar activity. To sum up, the results of this study allow us to propose three main conclusions. (1) The upper water temperature records of core MD01-2386 show obvious millennial-scale changes, which are closely coupled with the upper water temperature and atmospheric convection activity in the western equatorial Pacific, indicating consistent changes of the ocean-atmosphere coupled system in the western equatorial Pacific on the millennial-scale of the last deglaciation. (2) On the millennium scale in the last deglaciation, opposite changes in the air-sea feedbacks exist between the near-equator and off-equator areas of the warm pool, which may indicate relative changes of the atmospheric convevtion center but not a north-south shift of rain belt. (3) The planktonic foraminifera proxy records present significant cycling of 200−400 a centered at ~260 a and may reflect the linkage between centennial-scale solar activity and the upper water dynamics of the western equatorial Pacific.