Container Terminal Scheduling System is a random, dynamic, nonlinear complex systems. How to schedule in order to achieve MES seamless connectivity for management system and control system, which is reseach focus of MES currently. Aiming at the production process and production management features for container terminal, a thorough research on CIMS of container terminal enterprise is taken, the relationships of information exchange that among the plan layer, the execution layer and control layer are analyzed. On the basis of control theory and system engineering theory, and viewpoint of process control, a closed MES control system is build. It is established step by step to achieve seamless integration MES by intelligent modeling and control compensation of scheduling. A new and original way for realizing accurate and transparency management in the production process and production optimization is provided.