Joint clearance is unavoidable because it ensures successful assembly and deployment, but it also affects the dynamic response, stability, and pointing accuracy of large deployable space structures. This paper investigates the effects of clearance joints on the dynamic response of a beam-joint structure, a fundamental element of large deployable space structures. Vector form intrinsic finite element is employed to establish the structure’s motion governing equation to overcome the difficulties in modeling and solving of traditional finite element method led by contact behavior. The contact forces are modeled by the Lankarani and Nikravesh contact model and the modified Coulomb's friction model. First, a classical benchmark problem of a clamped-clamped beam is studied to validate the accuracy and efficiency of the model proposed. Then, a planar beam-joint structure with clearance joints is used to investigate the effects of clearance on the dynamic response. Subsequently, multiple simulation cases are executed to study the effects of different clearance factors on the dynamic structural characteristics. The results show that as the coefficient of restitution becomes small and the sliding friction coefficient gets large, more energy is dissipated, revealing their significant influence on the structural damping characteristics. Joint clearance enlarges the structure’s dynamic response, and larger clearance size and more clearance joints exacerbate these effects. The structure’s damping ratio becomes larger when the clearance size gets smaller. These results indicate that clearance joints have significant effects on the structure's dynamic characteristics, and they must be considered in the design and analysis of high-precision space structures.