A microscope system includes a light amount ratio changing unit for changing a ratio of the amount of light directed to a first optical path for directing an optical image of the sample to an eyepiece lens and a second optical path for directing an optical image of the sample to an image capturing unit, an image capturing controlling unit for controlling an exposure time of the image capturing unit, and a controlling unit for obtaining a first exposure time from the image capturing controlling unit, for calculating a second exposure time on the basis of the first exposure time and a second ratio of the amount of light, and for controlling the image capturing controlling unit to set the second exposure time as the exposure time if the light amount ratio changing unit changes to the second ratio of the amount of light.