A method of measuring natural frequency by excitation of a piezoelectric stack is proposed. In comparison with the traditional method that using a vibrating table or a hammer, the proposed method is nondestructive to the structure even when the structural damping is small and the displacement magnification factor is large, because the amplitude of the vibration is controlled to be exceptionally small. A cantilever of a high Q factor is designed to verify the method. An eddy current sensor and a lock-in amplifier are utilized to detect the displacement of the cantilever. The finite element analysis and the experimental result show that the proposed method can measure the natural frequency without destruction to the structure effectively.