The purpose of this study was to review the safety and efficacy of the minimally invasive percutaneous nephrolithotomy in the treatment of medullary sponge kidney patients with complex renal calculi. Sixteen medullary sponge kidney patients with complex renal calculi underwent minimally invasive percutaneous nephrolithotomy procedures in our center were entered into this retrospective study. The data analyzed included patients' demographics, stone burden, operative time, operative blood loss, length of hospital stay, complications according to the modified Clavien system, and stone-free rate. All the patients in this study had complex renal stones that included 14 multiple stones and 3 partial staghorn calculi. The mean stone surface area was 779.5±421.1mm(2). Preoperative urinary tract infection was noted in 5 (31.2%) patients. Minimally invasive percutaneous nephrolithotomy was successfully completed in 15 renal units in 14 patients. Two patients failed the procedure. The mean operative time was 87.3±32.3min. Mean hemoglobin drop was 25.3±16.5g/L. An initial stone-free rate of 60% was achieved after the procedure, and the final stone-free rate was 86.6% after auxiliary second look and/or shock-wave lithotripsy. Clavien grade I and II complications occurred in 3 (21.4%) patients including the one (7.1%) patient who required transfusion. All the complications were managed conservatively. No major complications occurred. This retrospective analysis confirmed that minimally invasive percutaneous nephrolithotomy was a safe alternative treatment for the medullary sponge kidney patients with complex renal calculi. This procedure provided an acceptable stone-free rate and low incidence of high-grade complications. Stone-free rate further could be further improved with auxiliary procedures.