A microscope device (1) comprises an illumination optical system (10,20) for illuminating a sample, a detection optical system (40) for receiving light from the sample, a detector (60) for detecting the light from the sample via the detection optical system and outputting a detection signal of the light, a data processor (66) for generating at least one of a three-dimensional refractive index distribution and a two-dimensional phase distribution in the sample based on the detection signal output from the detector, and a modulation element group that is provided at a position of a pupil or a position conjugate with the pupil in only the illumination optical system, and has light transmittance changing continuously within a surface of the pupil or within a surface conjugate with the pupil.