In order to properly perform smoothing depending on depth-of-field so as to provide a 3D image with improved display image quality, a microscope system comprises: a microscope device 1 for acquiring a plurality of observation images with different focal points; a 3D image constructing unit 17 for constructing 3D image data based on the observation images; a smoothing strength calculating unit 18 for calculating smoothing strength for smoothing the 3D image data, based on optical information of the microscope device 1; and a smoothing unit 19 for smoothing the 3D image data with the smoothing strength calculated in the smoothing strength calculating unit 18.