Improving operation efficiency of container terminal, is important for terminal operators. Meanwhile, the air pollution problem is increasingly serious in container terminal, with the establishment of the Emission Control Areas (ECAs) of China in 2015, environmental protection pressure is increasing to terminal operators. In order to comply with the ECA regulation, optimizing the operation efficiency, reducing air pollution emissions, which, is an urgent problem to terminal management in China. This paper based on the characteristic of Container Terminal Operation System (CTOS), including berth allocation problem, truck dispatching problem, and yard allocation problem, establishes the architecture of CTOS based on the Multi Agents System. A model and simulation on a port container terminal is built on the JADE platform to support the decision-making of container terminal, which can reduce air pollution emissions in port, and maintain service levels. CTOS allows the container terminal operator to be more flexible in their decision to meet the ECA regulation.