Abstract The Kuroshio transports large amounts of heat from the tropical to extratropical Pacific, playing a crucial role in regional climate changes. However, how the temperature and heat transport changes of the Kuroshio under a warming climate remain ambiguous. In this study, based on long‐term full‐depth observations during 1965–2020, we firstly reveal that there exists an enhanced warming trend in subsurface layer of the Kuroshio. The mean and maximum subsurface warming rates reach 0.18°C per decade and 0.30°C per decade, respectively, which are much higher than those of the Kuroshio surface and global average temperature. The enhanced subsurface warming contributes 73% of the Kuroshio heat transport increase. We further indicate that the subsurface warming signals originate from sea surface warming in the downstream Kuroshio Extension region. Our findings highlight that the pronounced Kuroshio subsurface warming has considerable implications for the regional climate and ecology changes.