Objective To study the biomechanical effect from different prosthetic materials used on unilateral maxillary defect repair by three dimensional finite element (FE) analysis method. Methods The maxillary unilateral defect model was reconstructed by medical image processing software MIMICS. The prosthesis was generated by mirroring technology. After processing, the FE unilateral maxillary defect model and healthy maxillary model were established to simulate stress distributions on the maxilla during occlusion. Results The maximum stress on maxilla using different repair materials was always found concentrated on the edge of maxilla connected with zygoma (the positions attaching zygolabialis and levator anguli oris). The minimum stress of from the maxilla edge on the repair side was 8.471 MPa by using tricalcium phosphate (TCP) composite. The maximum stress from the maxilla edge on the repair side was 17.55 MPa by using hydroxyapatite (HA) material. Conclusions Different repair materials had no significant effect on natural side of the maxilla after restoration, while a greater impact of force status on the repair side was found. The elastic modulus of different repair materials can be used as a basis for maxilla restoration in clinic.