Atmospheric and Ocean reanalysis products are handy tools for studying the past climate. However, the choice of these products could influence the outcome of the study. In this study, we compared two popular Ocean reanalysis products (ORAS4 and GECCO2) in the context of the Indian Ocean (IO) heat content variability. The region of interest is the southern tropical IO (STIO) as the region features a seasonal upwelling zone and the Indonesian Throughflow (ITF) is nearly aligned with it. The comparison mainly includes the trends in sea surface height anomaly, IO response to Interdecadal Pacific Oscillation (IPO), and the recent changing behavior of Indo-Pacific Oceans. Among the drivers of southern tropical Indian Ocean subsurface heat content (STIOSHC), the local atmospheric wind forcing seems to be contributing more to its variability in ORAS4 where as ITF seems to be contributing more in GECCO2. To get a deeper understanding of the local and remote influences, we distinguish the interannual variability in the STIOSHC due to local atmospheric contribution and ITF contribution by setting up an Indian Ocean model using ROMS and carrying out some experiments. We show that the interannual variability in STIOSHC contributed by local winds is higher in ORAS4 when compared to GECCO2 and it is mainly reflected in the western IO. In the eastern IO, in ORAS4, the local wind and ITF contributions to the STIOSHC variability are found to be comparable whereas in GECCO2, the ITF contribution is greater than that of ORAS4. In GECCO2, the local wind and ITF contributions are found to be more or less same whereas in ORSA4, the local wind contribution is noticeably higher than the ITF contribution. Also, the local wind and ITF contribution to STIOSHC are found to be out of phase with dominant time periods of 8 to 15 years. The high STIOSHC during first (second) half of the warming hiatus period is found to be contributed by ITF (local surface forcing). The sea surface height anomalies and sea surface temperature anomalies (SSTA) in ORAS4 at few key locations in the Indian Ocean are found to be more in line with observations than those of GECCO2. We posit that ORAS4 is more reliable than GECCO2 over the IO.