We have developed a three-dimensional non-Newtonian and non-isothermal flow analysis of the twin screw extruder (TSE) using the finite element method. This code can simulate the fully filled parts of several kinds of screw elements, such as full flight screws, kneading blocks, rotors and their combinations. A marker particle tracking analysis has also been developed to evaluate the mixing performance of the screw elements. In this paper, simulations for the kneading blocks in a co-rotating TSE were carried out. The screw configurations are combinations of 2-lobe kneading blocks with several stagger angles and disk widths. The effects of screw configurations on pressure and temperature distributions are examined. We also evaluate the dispersive and distributive mixing via stress magnitude and area stretch obtained by marker particle hacking analysis, Additionally, we discuss the desirable stagger, disk width and their combinations that promote the mixing performance.