A microscope system and an illumination intensity adjusting method that can automatically adjust an illumination intensity when a bright-field illumination system and a dark-field illumination system are simultaneously used are provided. The microscope system includes: a stage on which a specimen is placed; an objective lens that converges observation light from at least the specimen S on the stage; a bright-field illumination unit configured to emit bright-field illumination light that is illumination light aperture to the specimen for a bright-field observation; a dark-field illumination unit configured to emit dark-field illumination light that is illumination light aperture to the specimen for a dark-field observation; and an illumination intensity control unit configured to adjust an illumination intensity of at least one of the bright-field illumination light and the dark-field illumination light according to the illumination intensity of the other one.