A kind of discontinuous baffle, which had the same length as the non-baffle zone distance, was inserted in the unwound channel of a single screw extruder to enhance mixing in the screw channel. The periodic unit of the flow channel was modeled as a dynamic system of complex duct flow. The finite volume method was used to solve the three-dimensional flow of purely viscous non-Newtonian fluid. Fluid particle tracking was performed by a fourth-order Runge-Kutta scheme. The effect of the baffle height on the mixing kinematics was investigated numerically. Poincare sections were applied to reveal the different patterns and sizes of the KAM tubes. Distributive mixing was then visualized by the evolution of passive tracers initially located at different positions. The variance index and residence time distribution (RTD) were used to evaluate the statistical results. Among the four test cases, the results showed that the case with the baffle height equal to the screw depth had the largest chaotic mixing region, but the shortest mean residence time and the narrowest broadening of RTD under the same pressure gradient.