AbstractPolyether‐ether‐ketone (PEEK) is a high‐performance biomaterial, which can be used to fabricate dentures, mandible, and other human implants. However, when the material extrusion (MEX) method is employed to print parts using PEEK material, the parts are prone to warpage deformation, which affects the fabrication quality of PEEK parts. Moreover, the uneven temperature field adversely affects the crystallization of PEEK, causing the printed objects with hazel appearance which affects the beauty of the denture. In this paper, finite element analysis is initially performed to study the temperature and stress fields of PEEK under different printing parameters in MEX. Second, the response surface method is used to evaluate the accuracy of the simulation results. Furthermore, a mathematical model of the relationship between warping deformation and the affecting factors during MEX is obtained. The simulation and experimental results show that the temperature field, stress field, and final warping deformation are positively correlated with the extruded filament width, printing speed, and molding chamber temperature, while they are negatively correlated with the nozzle temperature. The impact of each parameter in a descending order is: extruded filament width, printing speed, molding chamber temperature, and nozzle temperature.