Tri-screw extruders are new extrusion equipments for food and polymer processing. Especially, there is one special circumfluence exists in center region only at cross section. In this study, the 2D transient and non-isothermal modeling of a tri-screw extruder is established by using Finite Element Method (FEM) with particle tracking technology to reduce the axial effects. The transient temperature and flow fields are calculated with a commercial code, Polyflow. Moreover, the effect of temperature rise due to viscous heating on the flow and mixing characteristics such as mixing index, segregation scale, mean and instantaneous time-averaged efficiency of mixing for the tri-screw extruder are carried out. The results show that in the special center region, the velocity and mixing index is small and viscosity and temperature are relatively big, indicating the poor mixing efficiency. When the heat transfers due to self-heating is considered, the dispersive mixing of the tri-screw extruder decreases, but the distributive mixing and stretching mixing efficiency all increase for the tri-screw extruder. In particular, the stretching effect of the fluid particles in the tri-screw extruder decreases due to the decrease of viscous dissipation when the non-isothermal model is employed.