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Despite the rapid warming in the south Indian Ocean (SIO) during the recent two decades, the upper 300 m of the tropical southwest Indian Ocean (SWIO) experienced significant cooling during 2005–2011. The decreasing rate of the observed temperature reached −0.50 ± 0.1°C/decade. Heat budget analysis reveals that the cooling trend over SWIO results from the competing effect between local air‐sea heat flux and horizontal heat advection. Moreover, all the three observational datasets indicate that in the subtropical SIO, a prolonged cooling event occurred beneath the thermocline during 2010–2016. Although there exist some discrepancies between the observations and estimating the circulation and climate of the ocean (ECCO) reanalysis before 2010, the observations and ECCO reanalysis agree in terms of the post–2010 temperature variability in the intermediate layer of the subtropical region, probably because of the better constraint of the ECCO assimilation product by the increased sampling of Argo floats in the deeper ocean. The heat budget analysis indicates that during the period 2010–2016, the decadal cooling in the 400–1,000 m layer is primarily modulated by vertical ocean advection, and the horizontal ocean advection makes a secondary contribution. This study expands our knowledge of the decadal temperature variability and heat balance in the SIO during the Argo era.