A high-resolution global ocean/sea ice model is used to investigate the modes of Arctic Ocean heat content variability for the period 1968–2007. A rotated empirical orthogonal function analysis is performed on the monthly mean vertically integrated heat content to investigate the mechanisms governing its spatiotemporal variations. In the model, 28% of the heat content variability is driven by the seasonal and interannual fluctuations of the atmospheric heat flux in the seasonally ice free regions. The heat flux variability associated with Atlantic Water advected through Fram Strait drives 31% of the heat content variability. Changes of temperature and circulation drive Fram Strait heat transport variability, and these two effects project on different modes and thus drive heat content variations in different parts of the Eurasian Basin. A second branch of Atlantic Water is modified in the Barents Sea and the variations of the heat flux associated with the Barents Sea water branch penetrating the deep Arctic yield heat content variations in the Eurasian Basin. The effect of the Bering Strait heat flux variations remains limited to the Chukchi Sea. Autonomous observing system may be able to capture the Arctic heat content variability. Sea surface temperature satellite observations combined with temperature profiles of the top 800 m in the deep Arctic covered by sea ice are sufficient to capture most of the variability signal. The results emphasize the crucial need for measurements in the Eurasian Basin.