A microscope system comprising: a microscope apparatus (100, 20; 200, 20; 300) including a correction device that corrects a spherical aberration, the microscope apparatus (100, 20; 200, 20; 300) obtaining image data of a surface to be observed of a sample in each of a plurality of states having different setting values of the correction device so as to obtain plural pieces of image data; and a computing device that calculates an evaluation value of the image data on the basis of each of the plural pieces of image data obtained by the microscope apparatus (100, 20; 200, 20; 300) so as to calculate evaluation values of the plural pieces of image data, the evaluation value indicating a larger value as the spherical aberration is corrected more satisfactorily, wherein for each of a plurality of Z-positions of an objective provided in the microscope apparatus (100, 20; 200, 20; 300, 20), the microscope apparatus (100, 20; 200, 20; 300) repeats a process of obtaining the plural pieces of image data in such a way that a distribution range and an average interval of the setting values of the correction device are narrowed in each repetition, the setting values being set in the plurality of states, and that a setting value of the correction device that corresponds to a maximum evaluation value calculated by the computing device is included within the distribution range, and the computing device calculates, for each of the Z-positions, a target value on the basis of the evaluation values calculated by the computing device and the setting values that correspond to the evaluation values, the target value being the setting value of the correction device for correcting the spherical aberration on the surface to be observed. a microscope apparatus (100, 20; 200, 20; 300) including a correction device that corrects a spherical aberration, the microscope apparatus (100, 20; 200, 20; 300) obtaining image data of a surface to be observed of a sample in each of a plurality of states having different setting values of the correction device so as to obtain plural pieces of image data; and a computing device that calculates an evaluation value of the image data on the basis of each of the plural pieces of image data obtained by the microscope apparatus (100, 20; 200, 20; 300) so as to calculate evaluation values of the plural pieces of image data, the evaluation value indicating a larger value as the spherical aberration is corrected more satisfactorily, wherein for each of a plurality of Z-positions of an objective provided in the microscope apparatus (100, 20; 200, 20; 300, 20), the microscope apparatus (100, 20; 200, 20; 300) repeats a process of obtaining the plural pieces of image data in such a way that a distribution range and an average interval of the setting values of the correction device are narrowed in each repetition, the setting values being set in the plurality of states, and that a setting value of the correction device that corresponds to a maximum evaluation value calculated by the computing device is included within the distribution range, and the computing device calculates, for each of the Z-positions, a target value on the basis of the evaluation values calculated by the computing device and the setting values that correspond to the evaluation values, the target value being the setting value of the correction device for correcting the spherical aberration on the surface to be observed.