The present disclosure discloses a scanning imaging system, comprising a transportation apparatus (40), a first imaging system (10), and a second imaging system (20). A distance between a ray beam (14) from a first ray generator (11) of the first imaging system (10) and a ray beam (24) from a second ray generator (21) of the second imaging system (20) in the transportation direction is roughly L. A controller (33) is configured to acquire, based on a count value of an encoding counter module (32), a correspondence relationship between data in a position of the inspected object (A) in the transportation direction which is collected by the first imaging system (10) and data in the position of the inspected object (A) in the transportation direction which is collected by the second imaging system (20), wherein a difference between a count value of the encoder (30) corresponding to the data in the position which is collected by the first imaging system (10) and a count value of the encoder (30) corresponding to the data in the position which is collected by the second imaging system (20) is roughly L/D. The present disclosure can achieve alignment of the DR data image and the CT data image in a simple manner.