A microscope system includes: a wavefront modulator that modulates a wavefront of light from a light source; an objective that irradiates a sample with light whose wavefront has been modulated by the wavefront modulator; a spherical aberration corrector that corrects spherical aberration caused by a difference between a refractive index of a medium between the objective and the sample and a refractive index of the sample; a refractive index calculator that calculates, for each wavelength of the light from the light source, an average refractive index of a medium between the objective and a condensing position of light emitted from the objective on the basis of an amount of the corrected spherical aberration; and a controller that controls the wavefront modulator to correct chromatic aberration calculated on the basis of the calculated average refractive index for each wavelength.