Signal to noise ratio and signal to background ratio are crucial factors for a confocal scanning fluorescence microscope to form high contrast and resolution images of thick tissues because of the low signal level and multiple scattering processes. So the suppression of stray light is very impertant. Based on the concept of information capacity and the results of the calculation of the signal to noise ratio and the transfer function of a confocal scanning fluorescence microscope, the relationships among the information capacity, signal to noise ratio and 3 D optical transfer function are analyzed. The results obtained is very useful for development of a confocal scanning fluorescence microscope.