An X-ray CT apparatus includes an X-ray radiation unit which applies a first X-ray having a first energy spectrum and a second X-ray having a second energy spectrum different from the first energy spectrum to a subject, an X-ray data acquisition unit which acquires first X-ray projection data of the subject based on the first X-ray and second X-ray projection data of the subject based on the second X-ray, and an image reconstruction unit which determines information about a difference between the first X-ray and the second X-ray with respect to an image of the subject, segments the image into at least two pixel areas based on the difference information, and sets part of the segmented pixel areas to a dual energy image obtained by a weighted subtraction process based on X-ray projection data having a plurality of energy spectrums.