Objective   To investigate the clinical effect of percutaneous nephrolithotomy (PCNL) in the treatment of complex calculi in fused kidney, ectopic kidney, malrotation, atrophic kidney and pyelonecalyceal deformity.Methods   The clinical data of 48 patients with kidney stones treated with PCNL in Hanchuan people's hospital from 2015 to 2019 were retrospectively analyzed. There were 14 cases of renal malrotation, 12 cases of repeated renal pelvis with complete or incomplete repeated ureter, 10 cases of horseshoe kidney, 8 cases of unilateral renal atrophy, 3 cases of cross fusion ectopic, and 1 case of pelvic kidney. After strict preoperative preparation, all patients were in prone or supine position, and the operation was performed in one stage.Results   After stage I PCNL, 39 patients (81%) achieved complete stone removal, and another 7 patients with residual stone also achieved stone-free state after extracorporeal shock wave lithotripsie, and the final stone removal rate reached 96% (46/48). During the operation, 25 patients were operated in supine position, and the time required from the establishment of percutaneous renal channel to the completion of operation was significantly less than that in prone position (P<0.05). Three cases needed to establish multiple channels; the mean hospital stay was 3 days (2～7 days). After surgery, 3 patients needed blood transfusion, and 2 patients developed perirenal pseudocysts, without intestinal fistula or vascular or visceral injury. Calculus analysis showed that 83% of the calculi were calcium oxalate calculi.Conclusions   PCNL can achieve good results in the treatment of stones with various renal malformations, such as fusion kidney, renal ectopia, malrotation, renal atrophy, renal pelvis and calyceal variation, etc., but it requires surgeons to have firm determination and skilled surgical skills.