Purpose Parathyroidectomy is beneficial in tertiary hyperparathyroidism (THPT) consequent to chronic renal failure. The craniofacial morphology of patients who undergo total parathyroidectomy and autologous transplantation (tPTX + AT) has not been widely studied. This study assessed the efficacy of tPTX + AT in THPT and evaluated possible improvements in craniofacial features. Methods This retrospective analysis included patients who were diagnosed with medically refractory THPT and had undergone tPTX + AT between September 2013 and May 2021. The VAS was used to evaluate improvements in various symptoms including bone pain and pruritus. Changes in serum calcium, phosphorus, alkaline phosphatase, and intact parathyroid hormone (iPTH) levels were also assessed. The impact of the procedure was assessed by comparing two-photon X-ray bone mineral density measurements obtained 1 year before and after surgery. Results The VAS of pain and pruritus decreased significantly on the first postoperative day ( P < 0.05). Calcium levels changed significantly (from 2.50 ± 0.22 mmol/L to 2.10 ± 0.26 mmol/L) on postoperative day 1 ( P = 0.0000); iPTH levels also declined substantially on this day, reducing from 211.00 (122.10, 252.80) to 5.04 (2.96, 9.40) pmol/L. Bone mineral density increased significantly across various regions including the greater trochanter of the femur, intertrochanteric area, total hip, and third lumbar vertebra ( P < 0.05). The angles between the upper incisor and mandibular plane and the lower lip and Ricketts E line (drawn from the tip of the nose to the soft tissue area) also improved ( P = 0.043, P = 0.001). Conclusion Total parathyroidectomy and autologous transplantation can rapidly alleviate bone pain and skin itching in THPT. It may also improve bone density and facial soft tissue.