Clearance, friction, and local elastic and plastic deformation of joint, which can be called joint effects, may cause nonlinear dynamic behaviour of mechanisms. In the paper, nonlinear dynamic behaviour of joint effects on a 2(3PUS+S) parallel manipulator was studied. There are 10 spherical joints in the 2(3PUS+S) parallel manipulator, and the dynamic characteristics of the spherical joints directly affect the overall output performance since they are connected to the moving platforms. Therefore, the joint effects of spherical joint and its effect are studied. To study the effect of the irregular clearance (size of the clearance varies with the attitude) of spherical joint due to manufacturing tolerance and wear, the spherical surface is approximated as an ellipsoid. In addition, the contact force models of spherical joint with variable contact stiffness were established under dry friction and lubrication condition, respectively. And then considering the contact forces of the spherical joints, the overall dynamic model of the 2(3PUS+S) parallel manipulator was established. Based on the overall dynamic model, the influence of joint effects on the dynamic characteristics of the 2(3PUS+S) parallel manipulator was studied, and the correctness of theoretical models was verified through experiments. The results from the simulation and experiments indicate that joint effects can cause nonlinear dynamic characteristics and have important influence on the dynamic performance of the 2(3PUS+S) parallel manipulator.