As common ultrasonic vibration system cannot meet the requirements of small size and large amplitude in vivo breaking stones, the design principle and method of ultrasonic vibration system with large amplitude and small volume were studied. Meanwhile, the displacement equation and stress equation of singlesection rod were received through the wave equation of arbitrary crosssection rod. The frequency equation of ultrasonic vibration system was deduced by the boundary conditions of vibration system. The ultrasonic vibration system for gravel was designed by the deduced frequency equation. The performances of the frequency of vibration system were obtained by FEM analysis and test. The results showed that the error of the designed frequency of vibration system was less than 3%, compared with the results obtained by FEM analysis and test. The maximum amplitude of the vibration system was 25 μm.