The purpose of this study was to analyze the biomechanical properties of implants made of different materials to replace missing teeth by using three-dimensional finite element analysis and provide a theoretic basis for clinical application. CBCT data was imported into the Mimics and 3-Matic to construct the three-dimensional finite element model of a missing tooth restored by an implant. Then, the model was imported into the Marc Mentat. Based on the variations of the implant materials (titanium, titanium-zirconia, zirconia and poly (ether-ether-ketone) (PEEK)) and bone densities (high and low), a total of eight models were created. An axial load of 150 N was applied to the crown of the implant to simulate the actual occlusal situation. Both the maximum values of stresses in the cortical bone and implant were observed in the Zr-low model. The maximum displacements of the implants were also within the normal range except for the PEEK models. The cancellous bone strains were mainly distributed in the apical area of the implant, and the maximum value (3225 μstrain) was found in PEEK-low model. Under the premise of the same implant material, the relevant data from various indices in low-density bone models were larger than that in high-density bone models. From the biomechanical point of view, zirconia, titanium and titanium-zirconia were all acceptable implant materials for replacing missing teeth and possessed excellent mechanical properties, while the application of PEEK material needs to be further optimized and modified.