Extrusion conditions and suitable screw configuration are key factors that affect protein reactivity and thus the properties of the blend. Fully revealing the whole extrusion process using numerical simulation is still a strong challenge due to the complexity of the flow field. In this paper, the flow behavior of protein under the action of kneading block and kneading block-reversing element was further revealed through the equivalent substitution, and the quality attribute of the extruded protein was also investigated. The results demonstrated the fluid pressure inside the barrel presented as a stepped and jagged increasing trend, and higher temperature and lower viscosity can be obtained at the screw root. The outlet pressure loss decreased when kneading block approached the outlet. Since the more complex fluid flow state at the location of the reversing element, more mechanical energy is transformed into internal energy, which amplifies the effect of temperature rise. Compared to the kneading block, the introduction of a reversing element can effectively improve the hardness and texturization of the extruded product, increase the brightness of color, and a better performance can be obtained at the backward reversing element. Overall, the consistency between the numerical simulation and the experimental results provided a research basis for the optimization of screw design combinations, and new theoretical support for the subsequent processing of meat analogs.