In this paper, analysis and control of the flexible multibody system using MATLAB is presented. The equations of motion of a flexible body are derived in terms of the modal coordinate. The rigid-flexible multibody dynamic solver is developed. Finite element information required to analyze motion of flexible bodies is imported from ANSYS. The modified finite element data, such as modal mass matrix, modal stiffness matrix and constraint mode shapes, is calculated in the solver. Since the solver is developed using MATLAB, it is very easy to connect with SIMULINK which is widely used to control motion of the multibody system. Several simulations are implemented to verify the developed solver. A control example is carried out and the usefulness of the developed solver is demonstrated.