The disclosure provides a system and a method for customs in-transit supervision. The system comprises: a port clearance subsystem (20) configured to collect and process information of a supervised object at a port; a risk management subsystem (40) configured to determine an in-transit supervision scheme for the supervised object based on a risk level of the supervised object; an in-transit supervision apparatus (10) configured to supervise the supervised object in transit according to the in-transit supervision scheme; and a central supervision subsystem (30) configured to conduct information interaction with the port clearance subsystem, the risk management system and the in-transit supervision apparatus and transmit instructions for controlling the subsystems and the apparatus. By introducing comparison between origin port information and destination port information and a risk management mechanism, the system and the method according to the disclosure improves the specificity, efficiency and intensity of supervision.