A method for manufacturing an apicoectomy guide plate includes: a) performing scanning to obtain a tooth jaw image model, a soft tissue image model, an alveolar bone image model, a tooth crown image model, and a tooth root image model that is defined with at least one affected area; b) calculating position relations of the tooth jaw image model corresponding to the soft tissue image model and the alveolar bone image model to determine at least one osteotomy and apicoectomy procedure, and establishing a guide plate model corresponding to the tooth jaw image model and the osteotomy and apicoectomy procedure; and c) outputting the apicoectomy guide plate, which includes a connecting portion corresponding to the soft tissue image model and the tooth crown image model, and at least one positioning portion corresponding to the affected area and comprising at least one pre-drilled hole.