Objective To compare the clinical effect of percutaneous nephrolithotomy and extracorporeal shock wave lithotripsy on treatment of complex urinary tract calculi. Methods 72 patients with complex urinary tract calculi were selected. 36 cases of taking percutaneous nephrolithotomy were included in nephroscopy group; 36 cases of taking extracorporeal shock wave lithotripsy were included in extracorporeal group. One-time success rate, intraoperative bleeding conditions and postoperative complications were compared. Results One-time success rate in nephroscopy group and extracorporeal group was 97.22% and 91.67%, without statistically significant difference (P>0.05); compared with nephroscopy group, intraoperative bleeding rate in extracorporeal group was lower while average operation time and hospital stays were shorter (P<0.05); total effective rate in nephroscopy group (91.67%) was significantly higher than that of extracorporeal group (72.22%) (P<0.05); urinary system infection, injury and recurrence rate in extracorporeal group was significantly lower than that of nephroscopy group (P<0.05). Conclusion Compared with extracorporeal shock wave lithotripsy, percutaneous nephrolithotomy has higher effective rate on treatment of complex urinary tract calculi, but may increase the postoperative complications and extend the hospital stays.