A container inspection system with CT tomographic scanning function, which is related to a large container inspection system for Customs, is disclosed, comprising: a radiation source; an annular rotatable rack with the radiation source provided at the outside thereof and rotated with it; an annular rack body for supporting the annular rotatable rack in a vertical plane; a driving device for rotating the annular rotatable rack; a detector array provided in the inner side of said annular rotatable rack and opposed to a side where the radiation source is provided; a transmission device passing through the annular rotatable rack and annular rack body, and transmitting a container truck to be detected in linear movement; a remote control device for controlling the operations of the radiation source, the driving device and the transmission device, and receiving/displaying the image signal obtained by the detector array. Not only can general inspection of the objects to be detected be undertaken, but also does repeated tomographic inspection of suspicious locations within the inspected objects, thus achieves effective accuracy improvement of the contrabands detection.