To operate a flexible mechanism in high speed its weight must be reduced as far as the structural strength does not decrease too much, but a light-weighted mechanism causes undesirable elastodynamic responses deteriorating the system performance. Besides, clearance within the connections of mechanisms causes rapid wear, increased noise and vibration. Even if the problems described above must be considered in the initial design stage, there has been no effective design process which takes account of the correlation between dynamic characteristics of flexible mechanism and the clearance effect at the joint. In this study, the generalized elastodynamic governing equations which include dynamic characteristics and boundary conditions of flexible mechanism are derived by variational calculus and solved by using FFM theory. To take the clearance effect at joint into account a new dynamic model is presented and also the method of modified stiffness/damping matrix is proposed to activate the dynamic clearance model, which cooperates with the developed governing equation very easily. As the results of this study, the proposed method(modified stiffness/damping matrix) to calculate clearance effect was proved to be superior to the existing one(force reaction method) in solution convergency and calculation performance. Besides this method can be easily adopted to the complex shape joint without calculation of reaction force direction.