A new approach for CFD-based aeroelastic simulation of rapidly morphing flight vehicles is presented is presented. The morphing vehicle consists of a number of components interconnected by actuators and contact constraints. Due to aerodynamic, inertial and actuation loads the overall structure undergoes large-displacement morphing. The method assumes that each component experiences large rigid-body displacements and small elastic deformations that are linear combinations of the individual normal modes. The structural equations of motion are based on a substructure modal synthesis method which applies fictitious masses at the interface coordinates. The modal synthesis method is expanded to allow large rotations between the structural components while keeping displacements and rotation compatibility at the interface coordinates. The compatibility equations are timedependent, and the inclusion of their time derivatives in the equations of motion brings introduces non-linear dynamic effects. The resulting generalized-coordinate nonlinear matrix equations of motion are embedded in a time-accurate CFD code. The vector of generalized forces includes aerodynamic forces from the CFD solution, inertial forces due to the modal accelerations and the relative component rotational velocities, and actuation forces. The computational process is demonstrated by two models: a two-wings-and-body configuration, where the wings are rotated rapidly from parallel position along a fuselage to perpendicular position; and a wing-body configuration where the wing is rotating about a hinge attached to a slender body from a parallel position to a perpendicular one. The morphing simulations demonstrate a robust and stable computational process that exhibits significant aeroelastic effects.