To rapidly analyze the dynamic characteristics of a compliant stroke amplification mechanism (CSAM) with completely distributed compliance, an analytical model based on the dynamic stiffness matrix with consideration of the damping effect is proposed. The natural frequency of the CSAM is optimized without attenuation of the amplification ratio based on this model. The optimized CSAM exhibits an approximately 112% higher natural frequency than the original mechanism along the main motion direction. The optimization result is verified through finite element simulation, with less than a 7% difference being observed. Moreover, the effects of frequency on the amplification ratio and input stiffness of the optimized CSAM are also discussed. The structural resonance is defined as the failure criterion of the optimized CSAM, and the sensitivity of the failure probability to manufacturing errors at different positions is analyzed. The findings show that the failure probability of the CSAM is more sensitive to parameters associated with the coordinates of the output stage and vertex.