Being considered the effect of the shearing and moment of intertia,the Hamilton system of free vibration of the Timoshenko cantilever beams was set up. The circular frequency for the two ends eigenvalue problem was calculated by using the method of precise integration of eigenvalue counting theory. Then the free vibration was analyzed. Based on the free vibration of the uniform Euler beams, The correctness of this method was verified through the calculation result comparison with this method and the traditional method. Then the circular frequency of the Timoshenko cantilever beams with the consideration under the effect of the shearing and the moment of intertia was calculated. The comparison results show that the method is simple,practicable and with good precision.