A medical image processing system that generates a subject image serving as a guide image for a procedure performed on a subject while viewing a fluoroscopic image taken by an X-ray imaging device, comprising a three-dimensional image acquisition unit configured to receive a three-dimensional CT image of the subject taken in advance by a CT device, and a three-dimensional MRI image of the subject taken in advance by a magnetic resonance imaging device, an image registration unit configured to perform registration between the three-dimensional CT image and the three-dimensional MRI image, a tissue structure extraction unit configured to generate a three-dimensional MRI specific-tissue image by extracting a predetermined specific tissue image from the three-dimensional MRI image after the registration, a parameter acquisition unit configured to acquire a value of predetermined type of parameter among multiple types of parameters set in the X-ray imaging device upon taking the fluoroscopic image, a projection calculation unit configured to use the value of the parameter acquired by the parameter acquisition unit to set a direction of light passage corresponding to a direction in which the X-ray passes through the subject in the X-ray imaging device, on each of the three-dimensional CT image and the three-dimensional MRI specific-tissue image, and to project the three-dimensional CT image and the three-dimensional MRI specific-tissue image along the direction of light passage, respectively, to generate two-dimensional projected images, and an image superimposition unit configured to generate a superimposed image in which the two-dimensional projected image of the three-dimensional CT image and the two-dimensional projected image of the three-dimensional MRI specific-tissue image are superimposed, and to display the generated superimposed image as the guide image. a three-dimensional image acquisition unit configured to receive a three-dimensional CT image of the subject taken in advance by a CT device, and a three-dimensional MRI image of the subject taken in advance by a magnetic resonance imaging device, an image registration unit configured to perform registration between the three-dimensional CT image and the three-dimensional MRI image, a tissue structure extraction unit configured to generate a three-dimensional MRI specific-tissue image by extracting a predetermined specific tissue image from the three-dimensional MRI image after the registration, a parameter acquisition unit configured to acquire a value of predetermined type of parameter among multiple types of parameters set in the X-ray imaging device upon taking the fluoroscopic image, a projection calculation unit configured to use the value of the parameter acquired by the parameter acquisition unit to set a direction of light passage corresponding to a direction in which the X-ray passes through the subject in the X-ray imaging device, on each of the three-dimensional CT image and the three-dimensional MRI specific-tissue image, and to project the three-dimensional CT image and the three-dimensional MRI specific-tissue image along the direction of light passage, respectively, to generate two-dimensional projected images, and an image superimposition unit configured to generate a superimposed image in which the two-dimensional projected image of the three-dimensional CT image and the two-dimensional projected image of the three-dimensional MRI specific-tissue image are superimposed, and to display the generated superimposed image as the guide image.