At present，the automated container terminals that have been built or are under construction in the world are mostly in the relatively mature layout mode of “double-trolley automatic quay crane + vertical yard arrangement end-side handling”，while the traditional layout mode of “single-trolley automatic quay crane + horizontal yard layout with side handling” is extremely rare. When there is no sufficient space between the container yard and the side，the operation mode of “ single-trolley automatic quay crane + IGV under-crane handling + horizontal yard layout with side handling ” can improve the efficiency of collaborative operation between single-trolley quay crane and IGV at the same time.The quay handling process flow and IGV traffic organization scheme，the key points of the logic behind the process flow which is adapted by each level of the system，the operation specification process and the key precautions are put forward to ensure that the automation operation is orderly，stable and efficient.