There is a special circumfluence in the center region of cross-section for a tri-screw extruder. To study the effect of the dynamic center region on the flow and mixing mechanism of the tri-screw extruder, 2D finite element modeling was used to reduce the axial effects. Based on the particle tracking technology, the nonlinear dynamics of a typical particle motions in the center region was carried out and the mixing process in the tri-screw extruder was analyzed with Poincaré maps. Moreover, mixing evaluations of the tri-screw and twin-screw extruders were analyzed and compared. The results show that there are many multiple and fractional excitation frequencies in the Fast Fourier Transform (FFT) spectrums, and it shows a chaotic motion in the center region. Poincaré section maps in the tri-screw show the better particles diffusive ability than those in the twin-screw extrude due to the excellent diffluent ability. Furthermore, the tri-screw extruder has the better dispersive, distributive mixing abilities and stretching mixing efficiency than the twin-screw extruder in the cross-section.