During glacial terminations, the role of cross-equatorial currents in the northward spreading of warm and salty waters is essential to the reach of the following interglacial state. In the western tropical Atlantic, where the interhemispheric North Brazil Current develops, most of the existing temperature records focused on the last deglaciation. Here, using a marine sediment core covering the last 305 kyr before present (BP), we present two records of the surface (mixed layer) and the subsurface (upper thermocline) temperatures based on organic proxies UK’37 and TEXH86, respectively. During the last three glacial terminations, these records exhibit large temperature increases especially in the subsurface layer. We suggest the combined influences of the thermal bipolar seesaw and the Agulhas Leakage, acting together to warm the interior South Atlantic, to explain the strong warming of the tropical western Atlantic thermocline (+5 °C) during these periods of reduced Atlantic meridional overturning circulation (AMOC). In addition, we propose an enhanced cross-equatorial gyre to elucidate the synchronous deglacial warming of the western and eastern sides of the tropical Atlantic. The resumption of the AMOC at the onset of the following interglacial leads to the release of heat stored in thermocline waters mainly in the whole South Atlantic, as highlighted by the sharp upper ocean cooling recorded at the end of the deglacial interval. The combination of this temperature record and previously published ones in the western tropical Atlantic confirms the strong sensitivity of the upper ocean to AMOC changes in this region.