A microscope system includes: an objective; a correction apparatus which corrects a spherical aberration; a controller which obtains a plurality of combinations of a relative position of the objective to a sample and an optimum value, which is a set value of the correction apparatus in a state in which a spherical aberration caused in accordance with the relative position has been corrected, calculates a function expressing the relationship between the relative position and the optimum value on the basis of the obtained plurality of combinations by interpolation, and calculates the optimum value according to an observation target surface of the sample, on the basis of the function and the relative position which is determined from the observation target surface; and a correction apparatus driving apparatus which drives the correction apparatus in accordance with the optimum value, which is calculated by the controller.