An object of the present invention is to provide a microscope system and an image processing method which are practical and capable of imaging a specimen efficiently in a short period of time and also ensuring reduction of the data amount of a generated image. Accordingly, the microscope system includes a storage section 24, 27 which stores identification information of a specimen 10A, a macro image and a micro image in a correlated manner, a stage member 11 on which the specimen as an observation target is mounted, an acquiring section 39B, 40 which acquires identification information of the specimen, a first display section 16, 22, 40, 47, 24 which displays a macro image of the specimen by reading a macro image correlated with the identification information from the storage section (or by imaging the specimen), a second display section 12 to 22, 47, 40, 24 which displays a micro image of the specimen by imaging the specimen, and an additional storing section 40 which additionally stores in the storage section in accordance with instruction from outside a micro image displayed on the second display section in a correlated manner with the macro image displayed on the first display section and the identification information acquired by the acquiring section.