Objective The three-dimensional ( 3D ) modeling of customized polyetheretherketone ( PEEK ) temporomandibular joint (TMJ) prosthesis was performed, and the stress distribution characteristics of prosthesis with three different condylar head shapes ( prototype, 80% prototype and cylindrical) were analyzed by finite element method, so as to evaluate the effects of three different condylar head morphology on stability, joint movement and articular fossa of PEEK total TMJ prosthesis. Methods The finite element analysis modelsⅠ,Ⅱ and Ⅲ of the cranio-maxillo facial and PEEK full TMJ prosthesis were established. Under four different occlusal conditions, i. e. , intercuspal position ( ICP), incisal clench ( INC), left unilateral molar clench ( LMOL), and right unilateral molar clench (RMOL), the maximum stress of the articular fossa prosthesis, condyle prosthesis and titanium scrows, the stress and strain distribution of the mandible, and the maximum displacement of the three models were analyzed. Results The maximum stresses of PEEK total joint prosthesis and screws in 3 models were 35. 22 MPa and 16. 73 MPa, respectively, which were lower than yield strength of the materials. The maximum stress of the mandible in modelsⅠ,Ⅱand Ⅲ were 41. 47, 42. 84 and 56. 92 MPa, and the strain was 3. 896× 10-3 , 2. 175 × 10-3 , 4. 641 × 10-3 , respectively. The maximum displacement of the three models was 209. 0 μm, which was located at the left mandibular angle of model Ⅲ. Conclusions PEEK TMJ prostheses with three different condylar head shapes all show uniform stress distribution, but the joint prostheses with 80% of the prototype condyle head shape have better mechanical effects. This study provides theoretical basis for the design of PEEK TMJ.