This study focuses on the temporal variation of dissimilarity in heat content (HC) anomalies in the upper 300 m of ocean (HC300A) in the equatorial Pacific (±10°N) and its response to the El Ni?o-Southern Oscillation (ENSO). The HC300A anomalies are derived from four ocean reanalyses that are commonly used in ENSO studies and are compared using a simple differencing method. The dissimilarity in HC300A is found to vary closely with the magnitude of ENSO (regardless of phase), meaning that it tends to be greater during strong ENSO events. However, the dissimilarity among ocean reanalyses persists after the event decays. This effect is more pronounced after strong events. The persistence of the dissimilarity after ENSO events is a result of a late maturation of the ENSO signal, its persistence, and the interruption of the signal decay due to follow-up ENSO events. The combined effect of these three factors slows down the decay of HC300A in the region and hence results in the slow decay of dissimilarity. It is also found that areas with a significant spread in vertical temperature profiles collocate with the ENSO signal during warm ENSO phases. Thus, differences in subsurface process reconstruction are a significant factor in the dissimilarity among ocean reanalyses during warm ENSO events.