Objective  To evaluate the safety and efficacy of stage-I minimally invasive percutaneous nephrolithotomy (MPCNL)for the treatment of upper urinary calculi complicated with pyonephrosis. Methods  From January 2012 to June 2013, a total of 26 patients with upper urinary calculi complicated with pyonephrosis were treated with stage?I MPCNL. Of the patients, 8 had upper ureteral calculi, 9 showed calculi in both kidneys, 13 suffered from renal pelvis calculi. Of the patients, 11 complained of low back pain at the affected side, 5 had fever before operation, 9 assumed bacteria culture positive in midstream urine. Results The mean operation time was 49.2±13.2 minutes in our patients. The stones were removed on one session in 22 cases(80.8﹪). Mean hospital stays was 8.38±0.98 days. Six patients confirmed bacteria culture positive in urine in the kidney pelvis, 1 patient confirmed positive blood culture after surgery. Eight patients appeard postoperative fever (Greater than 38 degrees Celsius), up to 39.6 degrees Celsius. Of the patients, 2 had a transient fever, 4 had a persistent fever last 1 to 3 days and 2 had a persistent fever last 4 to 5 days. Conclusion   Stage-I MPCNL is an effective, quick-recovery and safe treatment for upper urinary calculi complicated with pyonephrosis, as long we stick to the indications and standard procedures for the operation．