Introduction and importance: Kidney stones are a common condition treated in urology departments and rank first among hospitalized patients. Staghorn kidney stones are a particular type of kidney stone that fill or occupy most of the renal collecting system. They have a large stone load and are often associated with recurrent urinary tract infections and chronic renal insufficiency. Case presentation: We report a case of single-port robot-assisted laparoscopic pyelotomy combined with EMS (Electromagnetic Shockwave Lithotripsy) for surgical stone removal, and discuss and analyze it based on published literature. A 75-year-old woman visited our hospital in January 2024 due to right waist pain and hematuria. Computed Tomography (CT) indicated a stone approximately 6.1×5.8×3.5 cm in the right renal pelvis and calyces. Staghorn kidney stones are challenging to remove surgically, have a low stone clearance rate, and are prone to recurrence, making them one of the most difficult issues in urological surgery. Combined treatment effectively reduces the number of skin-renal passages, decreases the occurrence of injuries and complications, and improves the success rate of lithotripsy and the stone-free rate. Therefore, the patient underwent single-port robot-assisted laparoscopic pyelotomy combined with EMS surgical lithotomy and was discharged 7 days after the operation. There were no complications post-operation, and follow-up showed that the stones were completely cleared without any residue. Clinical discussion: The treatment of staghorn kidney stones requires a comprehensive approach to reduce the number of skin-renal passages and the occurrence of complications. Single-port robot-assisted pyelotomy combined with EMS lithotripsy can ensure the effectiveness of the surgery while reducing risks and enhancing patient recovery. Conclusion: For staghorn kidney stones, single-port robot-assisted pyelotomy combined with EMS stone removal is a safe and effective procedure with a beautiful incision, fewer complications, and excellent patient outcomes.