To investigate the influences of large deformation, clearance and uncertainty on the dynamic behavior and control accuracy of a manipulator, a methodology for establishing dynamics model of flexible manipulator with interval joint clearance is presented. Then an evaluation method for the dynamics model is proposed. In this work, the absolute nodal coordinate formulation is used to model the flexible components, while hybrid contact force model and Ambrósio friction force model are applied to construct revolute clearance joint. Meanwhile, intervals are used to characterize clearance size and Young’s modulus. The simulation results show that the flexibility and clearance can obviously affect the dynamic behavior and control accuracy of the manipulator. And the influence will be more significant as Young’s modulus decreases or clearance size increases. Uncertainty can reduce control accuracy and significantly affect the dynamic behavior of the manipulator.