The invention discloses a whole ship power balance control system and control method for a refrigerated container ship. The control system comprises an environmental data collector, a cold box controller, a cold box centralized controller, a fan controller, a fan centralized controller and a refrigerated container ship whole ship power balance control system. According to the system and the method, whole ship refrigerated containers are taken as a unified management object, the power consumption of all loads except the whole ship refrigerated containers is predicted, the refrigerated containers are dispatched, a ship power station is controlled, the whole ship power balance control is formed, the states of the refrigerated containers are separately monitored, the refrigerated containers are dispatched, compared with a method of maintaining the power balance of the refrigerated containers, the method of the invention has the advantages that the load prediction of other loads and the control of the ship power station are added, and the effects of reducing an installed capacity and reducing the operating cost are also more remarkable.