The invention discloses a ship power supply system, which is characterized in that the power supply system is an alternating current power system and is connected with the ship power network; The power supply system comprises a generator set, a battery energy storage system and an energy control module. The battery energy storage system comprises a battery system and a PCS, the battery system comprises a battery cell and a BMS for controlling the battery cell, the PCS is used for realizing bi-directional commutation, and the battery system is connected to the ship power grid through the PCS; The energy control module controls the generator set and the PCS according to the current-voltage data collected by the current-voltage transformer arranged at the generator set outlet line and the current-voltage transformer arranged at the energy storage system outlet line. On the other hand, the invention also discloses a control method of a ship power supply system realized by the system.