The invention relates to an intelligent operation management system and method for a container terminal, and belongs to the technical field of electronic information. The technical scheme is that the system comprises an EDI electronic receiving and transmitting subsystem, an intelligent plan subsystem, a gate subsystem, a basic operation subsystem, a fee collection management subsystem, a comprehensive statistical querying subsystem, and a yard crane operation subsystem; the EDI electronic receiving and transmitting subsystem achieves the receiving, importing and querying of various types of messages, generates corresponding messages, and transmits the messages to the Customs or each ship company; the EDI electronic receiving and transmitting subsystem comprises a data format module, a data processing module, a data querying module and an EDI code maintenance module. The beneficial effects of the invention are that the system starts from the reality, meets the business demands of the container terminal, and accords with the daily use habits; the intelligent and automatic system will greatly reduce the manpower cost and total operation cost of each terminal company after being put in operation, thereby further improving the operation efficiency of the terminal.