This paper presents the dynamic modeling and fuzzy sliding mode control for rigid-flexible multibody systems. To investigate the dynamic stiffening of rigid-flexible systems, a first-order approximate model of a flexible spacecraft system is formulated by using Hamilton’s principles and assumed mode method, taking into account the second-order term of the coupling deformation field. For highly flexible structural models, ideal surface sliding that produces pure rigid body motion may not be achievable. In this paper, the discontinuity in the sliding mode controller is smoothed inside a thin boundary layer using fuzzy logic technique to reduce the chattering phenomenon efficiently. Sliding mode control is insensitive to parameter variations and provides complete rejection of disturbances, but these advantages only hold in the sliding mode domain. However, when the actuators’ amplitude is limited by their physical constraints, the sliding mode domain will be restricted to some local domain near zero on the switching surface. Control input saturation is also considered in the fuzzy sliding mode control approach. The new features and advantages of the proposed approach are the use of new dynamic equations for the motion of flexible spacecraft systems and the design of fuzzy sliding mode control by taking into account the control input saturation. The classical sliding mode control case is also developed for comparison. Numerical simulations are performed to validate the proposed methods and to demonstrate that rotational maneuvers and vibration suppression are accomplished in spite of the presence of model uncertainty and control saturation nonlinearity.