Tropical subsurface circulation plays a key role in regulating heat and salt transport between the hemispheres, and in ocean–atmosphere interactions (e.g., El Niño-Southern Oscillation; ENSO). Therefore, understanding the past behavior of tropical thermoclines is important for predicting long-term global climate change. Here, we provide an orbital-scale thermocline temperature (TT) record based on Mg/Ca measurements of planktonic foraminifer Pulleniatina obliquiloculata in sediment cores obtained from the western equatorial Pacific (WEP) for the last 370 kyr. The vertical temperature gradient between sea surface temperature (SST) and TT in WEP showed weak positive correlations with the tropical Pacific zonal SST gradient in long-term trend and obliquity signal. The relationship of the two gradients does not coincide with modern ENSO variability, suggesting that the long-term TT variation depend primarily on another mechanism. Spectral analysis indicated that TT variability has strong signals in both the obliquity and precession bands. Since the obliquity signal is very weak in local insolation, the significant obliquity in TT variability implies an extratropical influence on tropical thermocline circulation. Therefore, our findings suggest that the subsurface circulation connecting the tropics and extratropics plays an essential role in orbital-scale tropical thermocline variability.