Objective To investigate the efficacy and safety of minimally invasive percutaneous renal puncture for the treatment of complicated kidney stones in children. Methods Retrospective analysis of 33 cases of complicated kidney stones in children admitted to our hospital, 21 males and 12 females, aged 5 to 14 years old, average 8.5 years old. The stones were located on the right side in 16 cases, on the left side in 13 cases, and bilaterally in 4 cases. The stone size was 2.1 cm×3.2 cm-3.7 cmx6.7 cm. All of them were treated with ultrasound positioning percutaneous renal pneumatic tract lithotripsy system, and stone removal was observed. All 33 cases in this group were successfully established by one puncture, including 4 cases with two channels and 4 cases with bilateral lithotripsy at the same time. 31 cases underwent percutaneous microcreative nephrolithotomy (MPCNL) in stage I and 2 cases in stage II. The operating time was 80-130 min, with an average of 92 min, and intraoperative bleeding was 30-80 ml, with an average of (61.5±12.3) ml, without blood transfusion. 1 case had a large stone residue treated with extracorporeal shock wave lithotripsy. The stone removal rate was 90.9% (30/33) in stage I and 96.9% (32/33) in stage II after lithotripsy. There were no serious complications such as pneumothorax, abdominal organ injury and hemorrhage. Postoperative fever was observed in 4 cases. There was no statistically significant difference in hemoglobin and blood creatinine values at 24 h postoperatively compared with those before surgery. The postoperative hospital stay ranged from 4 to 8 d, with an average of 5.4 d. The postoperative follow-up ranged from 3 to 18 months, with an average of 9 months, with no recurrence of stones. Conclusion Minimally invasive percutaneous nephrolithotomy is safe and feasible for the treatment of complicated kidney stones in children, with definite efficacy and the advantages of less trauma and faster recovery, and can be the treatment of choice for this disease.