A three-dimensional image processing apparatus includes a storage unit that stores data of a plurality of mask images and data of a plurality of contrast images, each of the plurality of mask images being obtained by radiographing a subject to be examined in a different direction before contrast medium injection, each of the plurality of contrast images being obtained by radiographing the subject to be examined in a different direction after the contrast medium injection, a reconstruction unit that reconstructs first three-dimensional image data from the plurality of mask image data and reconstructs second three-dimensional image data from the plurality of contrast image data, a positional deviation correcting unit that corrects positional deviation of the first three-dimensional image with respect to the second three-dimensional image on the basis of the comparison result between an anatomical structure of the first three-dimensional image data and an anatomical structure of the second three-dimensional image data, and creates third three-dimensional image data, and a processing unit that performs subtraction between the second three-dimensional image data and the third three-dimensional data and creates fourth three-dimensional image data.