While the crane system operate in port, one of main objective is to transport containers to the goal position as soon as possible. Because this is one of the biggest problem in terms of productivity of port, the container crane is operated by an expert operator until now. However recently an automatic control system with high performance is required to improve the performance of the crane system and to make high productivity. Therefore we developed an optimal controller based on Humoral Immune Algorithm with PID controller. The proposed system has a real time structure and can improve the performance such as anti-sway problem. Some computer simulations are implemented to assess the characteristics of the proposed controller.