An X-ray CT apparatus includes processing circuitry. The circuitry controls a voltage generator during non-helical scan to switch tube voltage, thereby causing an imaging to be performed separately with X-rays of a first energy and X-rays of a second energy. The circuitry generates first and second projection data sets, respectively. The circuitry performs image reconstruction based on the first and second projection data sets respectively, thereby generating first and second images respectively. The circuitry performs alignment processing to align the second image with the first image. The circuitry generates a third projection data set based on a processing result of the alignment processing. The circuitry performs transformation processing to transform the second and third projection data sets into projection data sets corresponding to reference materials. The circuitry performs image reconstruction based on the projection data sets after the transformation processing, thereby generating reference material images corresponding to reference materials.