Objective To make finite element analysis and compressive performance test on three-dimensional (3D) printed personalized poly-ether-ether-ketone (PEEK) condyle prosthesis, so as to analyze stress distribution characteristics and mechanical properties of the prosthesis, and to evaluate its clinical value and prospect. Methods The finite element models of PEEK condyle prosthesis, mandible and fixation screw were established by software such as CBCT, Mimics, Geomagic Studio, SolidWorks and ANSYS Workbench. The maximum mastication force was applied, and the maximum stress of the condyle prosthesis and screw, as well as the stress and strain of the mandible were recorded. In order to simulate the actual clinical situation, a special fixture was designed to test compression performance of the condyle prosthesis prepared by the fused deposition modeling (FDM) and selective laser sintering (SLS) at the rate of 1 mm/min. Results The peak stress of the PEEK condyle prosthesis was 10.733 MPa, which was located at the back of the condyle neck. The peak stress of 5 fixing screws was 9.707 5 MPa, which appeared on the 2# and 5# screws near the trailing edge of the mandibular ascending branch. The peak stress of both the prosthesis and the screw was smaller than its yield strength. The maximum pressure of the condyle prosthesis prepared by FDM and SLS was (3 814.7±442.6) N and (1 193.970±260.350) N, respectively. Compared with the SLS preparation, the FDM prepared prosthesis not only had higher compression strength but also better toughness. Conclusions The 3D printed personalized PEEK condyle prosthesis shows uniform stress distributions and good mechanical properties, which can provide the theoretical basis for PEEK as reconstruction material for repairing temporomandibular joint.