The analysis of actuating forces (or torques) and joint reaction forces (or moments) are essential to determine the capacity of actuators, to control the system and to design the components. This paper presents an inverse dynamic analysis algorithm for flexible multibody systems with closed-loops in the relative joint coordinate space. The joint reaction forces are analyzed in Cartesian coordinate space using the inverse velocity transformation technique. The joint coordinates and the deformation modal coordinates are used as the generalized coordinates of a flexible multibody system. The algorithm is verified through the analysis of a slider-crank mechanism.