The invention provides a customs in-transit regulation system and method. The custom in-transit regulation system comprises a port customs clearance subsystem, a risk management subsystem, an in-transit regulation device and a center regulation subsystem; the port customs clearance subsystem is used for collecting and processing the information of regulated objects at the position of a port; the risk management subsystem is used for determining an in-transit regulation pattern for the regulated objects according to the risk level of the regulated objects; the in-transit regulation device is used for regulating the regulated objects in transit according to the in-transit regulation pattern; the center regulation subsystem is used for performing information interaction with the port customs clearance subsystem, the risk management subsystem and the in-transit regulation device and sending an instruction which is used for controlling the port customs clearance subsystem, the risk management subsystem and the in-transit regulation device. According to the customs in-transit regulation system and method, a starting and destination port information comparison and risk management mechanism is introduced and accordingly the regulation pertinence and the regulation efficiency and strength are improved.