A tomography apparatus includes a data obtainer configured to obtain first image data at a first point and second image data at a second point using tomography, the tomography being performed by irradiating an X-ray to an object; an image processor configured to perform noise reduction based on at least one from among the first image data and the second image data, and to obtain a first reference image corresponding to the first image data and a second reference image corresponding to the second image data using a result of the performed noise reduction; and an image reconstructor configured to reconstruct a target image representing the object based on the first reference image and the second reference image.