Observations since the 1990s reveal widespread warming in the deep and bottom Arctic Ocean. It is historically attributed to geothermal heating, whereas the impacts of global and Arctic climate change on the deep and bottom Arctic Ocean warming remain unresolved. Our study demonstrates that during the recent decades, the Arctic Ocean deep water is warming at 0.020°C/decade in the Eurasian Basin between 2000 and 2600 m, exceeding what can be explained by geothermal heating. We find that the rapid warming in the deep Greenland Basin diminishes its cooling effect on the deep Eurasian Basin via the Fram Strait, leading to the warming in the deep Eurasian Basin. Meanwhile, the Lomonosov Ridge blocks this warming signal from reaching the deep Amerasian Basin, maintaining its relative slow warming rate of 0.003°C/decade. Our findings indicate that the deep Greenland Basin warming has already exerted obvious impacts on the deep Arctic Ocean.