Abstract: The technology of confocal microscope is widely applied in the three-dimensional profile metrology of the micro-electro-mechanical system and semiconductor device. This paper presents a novel confocal microscpe system based tunable-focus lens. By utilizing the changeable focal length of this lens instead of the traditional scanning methods in axial displacement, the system can realize scanning in axial direction without mechanical movement and eliminate the vibration caused by the axial scan movement. It can decrease the system complexity, and reduce the cost. A displacement stage based confocal system and a tunable-focus lens based confocal system were designed, and experiments were carried out for the two systems. Experimental results show that the confocal images of in-focus and out-of-focus of the two systems are similar, furthermore, the light intensity distribution along axial direction is basically the same, and that shows this new scan method is feasible.