A virtual microscope system capable of obtaining a stained sample image and a statistical data of spectra in a short period of time is provided, the virtual microscope system includes an image obtaining unit for obtaining a stained sample image, a spectrum obtaining unit for obtaining a spectrum of the stained sample image, an optical path setting unit for setting an optical path of a light flux passed through the stained sample with respect to the image obtaining unit and the spectrum obtaining unit and a control unit for controlling to repeat obtaining the stained sample image by the image obtaining unit and obtaining the spectrum of the stained sample image by the spectrum obtaining unit in the observation field of the stained sample to create a virtual slide and a spectrum table of the stained sample.