Two-implant-retained mandibular overdentures with magnetic attachments can provide an effective treatment modality for edentulous patients. In this study, a three-dimensional finite element analysis was used to compare the biomechanical characteristics of three different types of magnetic attachments in two-implant-retained mandibular overdentures. Flat-type, dome-type, and cushion-type of the magnetic attachments were designed to retain the overdenture. Four types of load were applied to the overdenture in each model: 100 N vertical and oblique loads on the right first molar and a 100 N vertical load on the right canine and the lower incisors. The biomechanical behaviors of peri-implant bone, abutment, and mucosa were recorded. In vertical incisors, vertical right canine, and oblique molar loading condition, the flat-type group exhibited the highest levels of maximum equivalent strain/stress in the peri-implant bone. The total deformation of mucosa and the maximum equivalent strain/stress in the oblique molar loading condition are about two times as the vertical molar loading condition. These results suggested that both cushion-type and dome-type of the magnetic attachments are better choices in two-implant-retained mandibular overdentures, and oblique loading is more harmful than vertical loading.