A microscope system includes: an illumination unit; a light control direction unit specifying quantity of light output from the illumination unit; a storage unit storing voltage-related information in which a direction value specified by the light control direction unit and a voltage value to be applied to the illumination unit are associated with each other and are set, the direction value being in an entire range that can be specified by the light control direction unit under each observation condition, the voltage value corresponding to the direction value; a light quantity control unit controlling the quantity of the emitted light; and a control unit acquiring the voltage value corresponding to the specified direction value from the voltage-related information corresponding to the observation condition, and allowing the light quantity control unit to control the quantity of light based on the acquired voltage value.