objective to explore the analysis of application of percutaneous nephrolithotomy clinical effect of treatment of patients with renal stones of complexity. Methods from April 2013 to December 2013 received treatment of complexity of 67 cases of kidney stones in 34 cases were randomly divided into treatment group and 33 cases of control group, control group patients mainly adopts the traditional open surgery treatment, the treatment group patients give percutaneous nephrolithotomy treatment. Results patients calculi clearance rate of treatment group was obviously higher than that of control group (p < 0.05); The intraoperative blood loss in patients with significant lower in treatment group than the control group (p <0.05); The treatment group patients bed activity time significantly shorter than the control group (p < 0.05); The incidence of complications in patients with treatment group was obviously lower than the control group (p < 0.05). Conclusion complexity of kidney stones in patients treated with percutaneous nephrolithotomy, can accelerate the recovery of patients, reduce the intraoperative blood loss, improve the calculi clearance rate, is worth popularizing widely in clinical.