The present disclosure discloses a scanning imaging system, comprising a transportation apparatus, a first imaging system, and a second imaging system. A distance between a ray beam from a first ray generator of the first imaging system and a ray beam from a second ray generator of the second imaging system in the transportation direction is roughly L. A controller is configured to acquire, based on a count value of the encoding counter module, a correspondence relationship between data in a position of the inspected object in the transportation direction which is collected by the first imaging system and data in the position of the inspected object in the transportation direction which is collected by the second imaging system, wherein a difference between a count value of the encoder corresponding to the data in the position which is collected by the first imaging system and a count value of the encoder corresponding to the data in the position which is collected by the second imaging system is roughly L/D. The present disclosure can achieve alignment of the DR data image and the CT data image in a simple manner.