We analyzed the non-Newtonian and non-isothermal flow in the melt conveying zone in co-rotating and counter-rotating screw extruder system with the commercial code, STAR-CD, and compared the mixing performance with respect to screw speed and rotating direction. The viscosity of fluid was described by power-law model. The dynamics of mixing was studied numerically by tracking the motion of particles in a twin screw extruder system. The extent of mixing was characterized in terms of the residence time distribution and average strain. The results showed that high screw speed decreases the residence time but increases the shear rate. Therefore higher screw speed increases the strain and has better mixing performance. Counter-rotating screw extruder system and co-rotating screw extruder has the similar shear rate with the same screw speed in spite of different rotating direction. However, the counter-rotating screw has good mixing performance, which is resulted from longer residence time than that of co-rotating screw extruder.