The biomechanical responses of a mandible supported by implants under normal and malocclusion were comparatively investigated. A three-dimensional finite element model for the magnetic attachment mandibular overdenture was established in two cases: normal occlusion and malocclusion. The biomechanical behaviors of the bone around the implant and the mucosa were recorded. In the case of malocclusion, the maximum elastic strain in the peri-implant bone is slightly larger than that under normal occlusion and both are within the threshold of physiological tolerance. The maximum equivalent stress in the mucosa is at the lowest level in a dome-type implant condition. The stress/strain value for patients with large tooth gap is slightly larger than that for other malocclusion patients. According to the analysis results, the patients with malocclusion can be implanted with implants as normal people, and the dome-type implant will be chosen as an effective treatment option.