The present disclosure provides a system, method and associated apparatus for autonomous vehicle transportation. The system includes: an operation system configured to generate a transportation plan for a vehicle and transmit the transportation plan to a vehicle controller of the vehicle; and the vehicle controller configured to control, in accordance with the transportation plan, the vehicle to autonomously move to a position of a checkpoint at an entrance to a target highway port, and interact with a checkpoint controller corresponding to the position of the checkpoint for autonomously passing the checkpoint; and control the vehicle to autonomously move from the position of the checkpoint to a specified loading/unloading position in the target highway port, and interact with a loading/unloading control apparatus for autonomous loading/unloading at the loading/unloading position. The system, method and associated apparatus can achieve fully autonomous goods transportation, save transportation costs and reduce driving security risks.