A photon counting X-ray CT apparatus according to an embodiment includes: data acquiring circuitry, and processing circuitry. The data acquiring circuitry is configured to allocate energy measured by signals output from a photon counting detector in response to incidence of X-ray photons to any of a plurality of first energy bins so as to acquire a first data group as count data of each of the first energy bins. The processing circuitry is configured to determine a plurality of second energy bins obtained by grouping the first energy bins in accordance with a decomposition target material that is a material to be decomposed in a imaging region, allocate the first data group to any of the second energy bins so as to generate a second data group, and use the second data group to generate an image representing a distribution of the decomposition target material.
