Number of researches on efficient terminal operation system applying RFID(Radio Frequency Identification) are in progress. However, RFID has limitations on tracking and providing accurate positions of containers. In this paper, to enhance the performance of the integrated terminal operation system, an efficient loading management of yard is proposed by applying RFID based RTLS(Real Time Locating System) that provides real time accurate positions of containers. It was found that a group based sequence system is more efficient than the existing individual sequence number system in the container yard In the group based sequence system, the containers in the same group should have similar characteristics such as port of destination(POD), size, weight, etc. In order to run this system, we proposed the parameters to the unspecified N bytes of RFID tag which are specified in ISO 18000 7. And then, we developed an integrated operation system of container terminal using RFID. The proposed system reduces the ship turnaround time in ubiquitous port environments.