A method for setting a scanning protocol and an apparatus thereof are provided. The method includes: creating a plain film positioning image receiving a point or a line or a region of interest on the plain film positioning image input by an operator generating a region to be matched, based on the point or the line or the region of interest determining whether there is pre-stored reference image having a matching degree greater than a preset threshold by comparing pre-stored reference images with the region to be matched obtaining a reference image in the case that the reference image has a matching degree greater than the preset threshold selecting a scanning protocol corresponding to the reference image based on a preset correspondence between reference images and scanning protocols and completing a setting of the scanning protocol in the case that there is the scanning protocol corresponding to the reference image.
