A microscope system has a VS image generation means for generating a virtual slide image of a specimen which is constructed by mutually connecting a plurality of microscope images with a first photomagnification photographed and acquired whenever an objective lens and the specimen are relatively moved in a direction perpendicular to the optical axis and which represents the entire image of the specimen, an object-of-interest set means setting an object of interest with respect to the entire image of the specimen represented by the VS image, and a three-dimensional VS image generation means for generating a three-dimensional VS image which is constructed by connecting the microscope images at different focal positions in accordance with the same focal position and which is constructed from the microscope images with a second photomagnification higher than the first photomagnification and represents the image of the object of interest.