In this paper, a parallel solution scheme for calculating inverse dynamics independent to member stiffness of link systems is described. The solution scheme is developed by using the Finite Element Method, which evaluates the entire system as a continuum by subdividing it into finite elements. It calculates nodal force by evaluating the equation of motion in a matrix form, and the information from the entire system can be handled in parallel. Therefore, the torque curves can be obtained seamlessly without changing the numerical algorithm, even in such cases where the dynamics of the link systems would gradually change. Moreover, the inverse dynamics of link systems with various stiffness values can be obtained similar to rigid link systems. In this paper, the kinematics of the link systems are calculated in order to obtain a target trajectory required for calculating the inverse dynamics, by considering stiffnesses of the finite elements. Both algorithms for calculating kinematics and inverse dynamics are combined into a single program. Some numerical tests carried out to simple link systems show the validity of the proposed scheme in applying as a unified scheme independent to member stiffness values.