The coupling effects of flexible joints and clearance on the dynamics of a robotic system were investigated. A numerical analysis was undertaken to reveal the coupling effects between flexible joints and clearance. The nonlinear spring-damping model and Coulomb model were applied to characterize the contact characteristics of the clearance, and a model for the flexible joint was formulated using the equivalent spring theory. An accurate robot model was established based on the clearance and joint flexibility characterization. The dynamic equation of a robot was obtained according to the Newton-Euler method. A comparative analysis was performed to assess the impacts of both the joint action of clearance and flexible joints and varying joint clearance values on the performance of the robot. The results showed that the coupling effects of flexible joints and clearance had a negative impact on the system dynamic performance. The amplitudes of the dynamic responses caused by the clearance are weakened by the flexible joint, but it leads to the lag of the system response. This study served as the theoretical foundation for exploring precise control techniques in robotics research.