In one embodiment, a medical image processing apparatus which analyzes blood flow dynamics in a predetermined region of a subject, the blood flow dynamics being generated from medical images obtained by imaging the predetermined region in time sequence over a plurality of time phases. The medical image processing apparatus includes memory circuitry configured to store a program; and processing circuitry configured to correct pixel values of a second medical image according to an amount of deformation of the second medical image when the second medical image is aligned with a first medical image by executing the program read out from the memory circuitry, the first medical image and the second medical image being among the medical images in the plurality of time phases.