The invention relates to an orthogonal linear scanning CL imaging system and an analysis method, and belongs to the field of scanning imaging. An X-ray source is positioned at the bottommost end, andhas two degrees of freedom, i.e., the X-ray source moves left and right and up and down and emits a cone beam X-ray upwards; a carrying stage is positioned above the X-ray source, and can implement plane translational motion and rotating motion; a flat panel detector is positioned above the carrying stage, and has two degrees of freedom, i.e., the flat panel detector moves left and right and up and down and synchronously receives the attenuated X-ray. The method comprises the steps that: in a first step, an object is fixed, the flat panel detector and the ray source take relatively parallel motion along sliding rails and acquire one group of projection data; in a second step, after the object rotates by 90 degrees in a plane of the carrying stage, the flat panel detector and the ray sourcealso take relatively parallel motion and acquire a second group of projection data. According to the orthogonal linear scanning CL imaging system and the analysis method, an amplification ratio and view field size can be regulated according to detection demands so as to adapt to different detection demands. By adopting orthogonal linear CL scanning, CL resolving power in two directions can be obtained.