AbstractIt has been reported that the Southern Hemisphere oceans experienced rapid warming during the decade‐long global surface warming slowdown (2003–2012) and the earlier period of the Argo record (2006–2013). In this study, we analyze updated observations to show that this rapid warming has slowed down, leading to less contribution of the Southern Hemisphere oceans to the global ocean heat storage (∼65% over the available Argo period 2006–2019). Two warming hotspot regions, the southeast Indian Ocean and South Pacific Ocean, have experienced cooling over 2013–2019. This decadal shift is related to variations in the Southern Annular Mode and Interdecadal Pacific Oscillation. The isopycnal deepening (shoaling) forced by changing winds dominated the regional ocean temperature changes over the earlier warming (later cooling) period. Our finding demonstrates how decadal variability modulates long‐term climate change and provides important observational information for the ongoing calibration of decadal prediction systems.