In this paper, Finite Element Method (FEM) is proposed for application to a control system of link mechanisms. The control software using FEM can deal with a sudden change in hardware, and is capable of expressing lack or disability of constituent members of the system only by changing input data since the entire system is subdivided into discrete elements and evaluated as a continuum. It handles the information of the entire system in parallel, which is useful especially when controlling hyper-redundant manipulators. The real-time control by using FEM became possible by applying the Shifted Integration technique, which produces the higher computational efficiency in the finite element analyses of framed structures including static and dynamic collapse problems. A single link structure of a pin joint and a rigid bar is expressed by shifting the numerical integration point in two linear Timoshenko beam elements. This paper describes the modeling of link mechanisms by using the Shifted Integration technique, and a numerical scheme to obtain joint torque curves in n-link mechanism based upon Cartesian coordinates is derived. A simulation test on 8-link mechanism by FEM is carried out and the joint torque curves are compared to those obtained by conventional Newton-Euler method.