We analyzed the non-Newtonian and non-isothermal flow with Carreau-Yasuda viscosity model in co-rotating and counter-rotating twin screw extruder systems. The mixing performances with respect to the screw speed, the screw pitch, and the rotating direction have been investigated. The dynamics of mixing was studied numerically by tracking the motions of particles. The extent of mixing was characterized in terms of the deformation rate, the residence time distribution, and the average strain. The results showed that the high screw speed decreases the residence time but increases the deformation rate. Small screw pitch increases the residence time. It is concluded that the high screw speed increases the dispersive mixing performance, while the small screw pitch increases the distributive mixing performance. Co-rotating screw extruder has the better conveying performance and the distributive mixing performance than counter-rotating screw extruder with the same screw speed and pitch. Co-rotating screw extruder developed faster transport velocity and it is advantageous the flow characteristics to the mixing that transfers polymer melt from one barrel to the other barrel.