By means of a recursive formulation method, a generalized impulse–momentum-balance method, and a constraint violation elimination (CVE) method, we propose a new global simulation method for flexible multibody systems with kinematic structure changes. The constraint equations of a pair of adjacent bodies, considering body flexibility in Cartesian space, are derived for a recursive formulation. Constraint equations in configuration space, which are obtained from the constraints presented in this paper via recursive formulation, are very useful for modeling different kinematic structures and impacting governing equations. The novelty is that the impact governing equations, which calculate the jumps of generalized velocities, are modified by taking velocity-level CVE into consideration. Numerical examples are given to validate the presented method. Simulation results show that the new method can effectively suppress constraint drifts at the velocity level and stabilize constraint violations at the position level.