An endoscope system includes an insertion portion, an objective optical window, an image pickup device, a position/direction detection section that acquires position information of the objective optical window, and a memory that records the subject internal image acquired by the image pickup device in association with the position information of the objective optical window. The endoscope system aligns the position information of the objective optical window with a reference position of a predetermined organ in the subject in a coordinate system of a three-dimensional model image based on an amount of change or the like of the subject internal image information in the subject and generates an image with the subject internal image pasted onto the two-dimensional model image of the predetermined organ which is the three-dimensional model image two-dimensionally developed in which the position of the objective optical window is associated with the position in the coordinate system.