The X-ray data processing apparatus to estimate a true value from an X-ray count value detected by the pixel array X-ray detector of a photon counting system includes a management unit 210 to receive and manage a detection value for each detection part, an effective area ratio calculation unit 230 to calculate a ratio of a detection ability under the influence of the charge share to an original detection ability in the detection part as an effective area ratio of the detection part using data regarding the detection part and data regarding an X-ray source and a detection energy threshold value, and a correction unit 250 to correct the managed count value using the calculated effective area ratio to estimate a true value.