The persistent energy imbalance at the top of the atmosphere, inferred from satellite measurements, indicates that the Earth’s climate system continues to accumulate excess heat. As only sparse and irregular measurements of ocean heat below 2000 m depth exist, one of the most challenging questions in global climate change studies is whether the excess heat has already penetrated into the deep ocean. Here we perform a comprehensive analysis of satellite and in situ measurements to report that a significant deep-ocean warming occurred in the subtropical South Pacific Ocean over the past decade (2005–2014). The local accumulation of heat accounted for up to a quarter of the global ocean heat increase, with directly and indirectly inferred deep ocean (below 2000 m) contribution of 2.4 ± 1.4 and 6.1–10.1 ± 4.4%, respectively. We further demonstrate that this heat accumulation is consistent with a decade-long intensification of the subtropical convergence, possibly linked to the persistent La Niña-like state.