The invention discloses a heating system of a fuel oil deep tank of a ship. A transverse heat-insulation partition with openings is arranged on a lower half zone of the fuel oil deep tank; heating pipes are respectively arranged on the partition and at the bottom of the fuel oil deep tank and are respectively connected with a heat supply system; temperature sensors are respectively arranged in an upper district and a lower district, and the fuel oil deep tank is divided into the upper district and the lower district by the partition; temperature signals of the temperature sensors are transmitted to the heat supply system and are used for controlling heat supply. The heating system has the advantages that the temperatures of the inside of the fuel oil deep tank can be respectively effectively controlled, consumption of saturated steam can be greatly reduced in actual shipping procedures of the ship, energy waste can be reduced, and accordingly the energy utilization efficiency of the container ship can be improved in the shipping procedures.