With the rapid development of container transport industry, container terminal systems have become more and more busy. Some measures and facilities are taken to improve the container throughput, such as Mega Ship, Mega Crane, Deep water Port, Automatic Container Terminal, Mobile Port, Dock Type Berth and Floating Berth. This paper deals with the transshipment transport problem in a container terminal arising from the usage of Mega Ship. We introduce the Berth Allocation Planning problem considering transshipment of ship to ship and formulate a mathematical model with different number of Quay Cranes in berth. A hybrid multistage operation-based Genetic Algorithm (h-moGA) with a priority-based encoding method is proposed. To demonstrate the effectiveness of the proposed h-moGA approach, numerical experiments are carried out and the best solution to the problem is obtained.