Objective To compare the therapeutic effect of percutaneous nephrolithotripsy(PCNL) and transureteroscopic in the treatment of patients whose diameter of renal calculi was ≤3 cm．Methods Analysis the treatment methods and curative effect of 243 cases of patients with kidney stones (diameter≤3cm) in our department from March 2011 to October 2012. One hundred twenty cases underwent the ureteroscopy Holmium laser lithotripsy (observation group) and 123 cases underwent percutaneous nephrolithotomy with holmium laser lithotripsy (PCNL) (control group). Operative time, postoperative complications, decreased hemoglobin values, postoperative indwelling catheter time and hospital expenses were compared in this two groups.Results The diameter of stone in observation group is (2.4 ± 0.9) cm, the control group was（2.3±0.9）cm. The difference of the two groups was not statistically significant (P＞0.05).There were 80 patients operated with the soft lenses in the observation group and five cases suffered fever. No serious complications such as bleeding and renal ureteral injury were observed. In the control group, there were four cases with fever, three cases bleeding obviously in and after operation, including two cases recovered after conservative treatment. Another one case recovered by selective renal artery embolization. In the observation group, the differences of the stone size, postoperative complications were not statistically significant  when compared with control group (P> 0.05). The postoperative indwelling catheter time（5.0±2.4)d , hospital expenses(13477.2±1754.3) and decreased hemoglobin values（0.25±0.1)g/L in the observation group were respectively lower than the control group (7.0 ± 3.7) d, (25453.1 ± 1763.5), (15.6 ± 7.1) g/L. Observation group on operation time was (105.2 + 38.2) higher than the control group (95.5 + 18.3).The differences was statistically significant (P <0.05). Conclusion The treatment effect of lithotripsy under ureteroscope for the patients with kidney stones (diameter≤3cm) is similar with PCNL. Meanwhile, lithotripsy under ureteroscope takes the advantage of less trauma, fewer hospital days, low treatment costs and low incidence of complications.