Provided is a medical image processing apparatus allowing the generation of image data by changing the reconstruction conditions in correspondence with the positional relation of an observation target based on the projected data chronologically acquired by an X-ray CT scanner. The medical image processing apparatus includes a photographing unit, a reconfiguration processing unit, an extracting unit, and an analyzing unit. The photographing unit scans the flexible site of the living body configured from multiple parts in order to acquire projected data. The reconfiguration processing unit carries out reconfiguration processing on the projected data and generates image data of the flexible site regarding the plurality of timing points. The extracting unit extracts the plurality of components configuring the flexible site from the respective image data. The analyzing unit obtains the positional relation of the plurality of components.