Abstract: The present invention utilizes aperture array element and vari-focus optical element in confocal microscopy system. With the aperture array element lateral scanning property can be obtained and with vari-focus optical element axial scanning property can be obtained. Especially Micromirror Array Lens is used as a vari-focus optical element, fast and extended depth of focus scan range can be obtained. Thus the present invention of confocal microscopy with the vari-focus optical element increases scan speed of confocal microscopy system. The confocal microscopy system of the present invention comprises an illumination source, an aperture array element, a vari-focus optical element, an objective lens element, a photosensitive optical sensor device. With these elements, confocal microscopy is performed to get three dimensional images.