Most congenitally missing teeth are often complex, and implant restoration is usually the best treatment option for them. A reasonable implant restoration design that takes into account the patient’s oral condition is the key to guaranteeing the final outcome. This case shows the design and procedure of implant restoration for congenitally missing teeth with severe bone deficiency. A case of congenital loss of most teeth with insufficient width of the alveolar ridge in the anterior region in the labiolingual direction and a severe lack of vertical height of the alveolar ridge in the premolar region was selected. Preoperatively, the restorative plan was reasonably designed, the treatment plan was arranged, and the final restorative approach was determined. The patient’s teeth could not be retained in the mouth were extracted, and the treatment of the remaining affected teeth was perfected. After the treatment was completed, the maxillary sinus floor was lifted bilaterally by trans-lateral windowing, and the sinus cavity was filled with a mixture of OSTEON® bone powder and RTR® bone powder and the patient’s autologous blood. The window is covered with a resorbable collagen membrane and tightly sutured with a reduction suture. Six months after implant placement, a second-stage surgery was performed to complete the established treatment plan and finalize the upper restoration. The mucosa of the sinus floor was intact after simultaneous implant placement, and the vertical height of the alveolar ridge in the implant area increased significantly by about 10 mm. 6 months after surgery, the bone volume was well maintained, with less than 1 mm of bone resorption. After the final crown restoration was completed according to the preoperative design restoration plan, the porcelain crown had good morphology, color and function; the soft tissue had good morphology and color. Most of the congenitally missing teeth are complex, and the preoperative restoration plan should be reasonably designed to avoid the implant sites with severe bone deficiency; the maxillary sinus floor lift through the lateral wall is an effective and reliable procedure to solve the severe vertical bone deficiency in the maxillary posterior region, and its application can reduce the risk of implantation and ensure the success rate of implantation; the simultaneous implant placement can shorten the treatment period and simplify the treatment procedure.