Objective To analyze the lithotripsy effect and complications of mini-percutaneous nephrolithotomy (mPCNL) in the treatment of patients with upper urinary stone. Methods From Jan. 2010 to Jan. 2011, a total of 90 patients with upper urinary stone in our department were taken as the clinical research objects, and they were randomly divided into A group (45 cases) and B group (45 cases). Patients in the A group were given mini-percutaneous nephrolithotomy, and the other patients in the B group were given percutaneous nephrolithotomy (PCNL). The intraoperative blood loss, operation time, hospital stay and stone size were recorded, the total stone clearance rate, upper stone clearance rate and incidence rate of postoperative complication in the two groups were compared. Results The intraoperative blood loss in the A group was lower than that in the B group, the hospital stay in the A group was shorter than that in the B group, the stone size in the A group was smaller than that in the B group, the operation time in the A group was longer than that in the B group, and their differences were statistically significant (P<0.05). The total stone clearance rate in the A group was 73.33% which was lower than that in the B group 91.11%, and their difference was statistically significant (P<0.05). The incidence rate of postoperative complication in the A group was 0.44% which was higher than that in the B group 17.78%, and their difference was statistically significant (P<0.05). Conclusion mPCNL whose characteristics are smaller wound, longer operation time, rapider postoperative recovery and more complications, is suitable for cleaning smaller stones. PCNL whose characteristics are higher stone clearance rate, shorter operation time and less incidence rate of complication, is suitable for cleaning bigger stone.