Environmental protection and energy saving pressure press the increasing attention of container terminal operators. In order to comply with the more and more strict environmental regulation, reducing energy consumption and air pollution emissions, meanwhile, optimizing the operation efficiency, which, is an urgent problem to container terminal operator of China. This paper based on the characteristic of Container Terminal Operation System (CTOS), which includes several sections of container product processes, consist of berth allocation problem, truck dispatching problem, yard allocation problem and auxiliary process. Dynamic energy consumption and emissions characteristic of each equipment and process is modelled, this paper presents the architecture of CTOS based on the multi agent system with early-warning model, which is based on multi-class support vector machines (SVM). A simulation on container terminal is built on the JADE platform to support the decision-making of container terminal, which can reduce energy consumption and air pollution emissions, allows the container terminal operator to be more flexible in their decision to meet the Emission Control Area regulation and Green Port Plan of China.