The medical image processing apparatus according to the embodiment comprises a photographing unit that scans the flexible sites of the living body including the plurality of components and obtains the projected data, a reconstruction processing unit that carries out reconstruction processing on the projected data and generated first image data of the plurality of timing points of the flexible sites, and an analyzing unit that compares the first image data of the plurality of timing points and the second image data showing the flexible sites, thereby specifying the data with the timing point shown in the second image data from among the first image data of the plurality of timing points.