A medical observation system includes: a position information storage portion configured to perform processing for storing first position information indicating an initial position of an object for executing treatment in a three-dimensional image generated using a plurality of tomographic images of a subject; a movement detection portion configured to detect movement of the object; a position information acquisition portion configured to acquire second position information indicating a present position of the object in the three-dimensional image when the movement of the object is detected; and a display image generation portion configured to update a position of the object in the three-dimensional image from the first position information to the second position information in a case that the second position information is acquired, and generate an image superimposed on the three-dimensional image or on a pseudo fluoroscopic image generated based on the plurality of tomographic images.