The objective of the study was to compare the therapeutic outcomes between the ultrasonography-guided (USG) and the fluoroscopy-guided (FG) mini-percutaneous nephrolithotomy (MPCNL) for the treatment of large or complex upper urinary tract stones (S.T.O.N.E. scores 5-11) in patients with autosomal dominant polycystic kidney disease (ADPKD). 45 ADPKD patients who were suffering from large or complex upper urinary tract stones (S.T.O.N.E. scores 5-11, mean score 7.6) in 45 renal units were accrued into this retrospective study. They were treated by either USG (20 patients) or FG (25 patients) MPCNL in our center. The treatment results as well as the complications according to the modified Clavien system were assessed and compared. The FG MPCNL group had a higher success rate in accessing the targeted calyces than the USG MPCNL group (96 vs. 70 %, p = 0.048). There was no significant difference observed between the two groups with respect to the operative time, the mean hemoglobin drop, and the stone free rate. The overall operative complications and the perioperative blood transfusion rates were significantly higher in the USG than the FG MPCNL groups, 71.4 vs. 29.2 %, p = 0.011, and 35.7 vs. 4.2 %, p = 0.018, respectively. There was no significant difference between these two groups in terms of major complications (Clavien score 3a-4a) (p = 0.542). In our center, the FG MPCNL was a superior modality to the USG MPCNL in the treatment of large or complex kidney stones in the ADPKD patients. It resulted in higher successful calyceal punctures and less operative complications.