Objective: To comparative analysis the clinical effects of the traditional pneumatic ballistic lithotripsy and flexible ureteroscope holmium laser lithotripsy on the treatment of upper urinary tract calculi. Methods: 80 patients who were suitable for flexible ureteroscope lithotripsy were equally and randomly divided into observation group and control group, the observation group were used flexible ureteroscope holmium laser lithotripsy, and the control group were given traditional pneumatic ballistic lithotripsy. Results: The operative time and postoperative hospital stay were significantly less than the control group (P < 0.05), but the total medical cost of the observation group was higher than that of the control group (P < 0.05). The stone clearance rate of the observation group was significantly higher. Followed-up 1 month, the stone-free rate of the observation group was significantly higher (P < 0.05). Followed-up 3 month, The severe bleeding, ureteral perforation, septic shock overall complication rate between the two groups had no significant difference (P > 0.05). the satisfaction of the observation group was 95.0%, so that was 75.0% in the control group that compared had statistically significant difference (P < 0.05). Conclusion: Flexible ureteroscope holmium laser lithotripsy for treating upper urinary tract calculi can improve the success rate of lithotripsy with less trauma, it can improve patient satisfaction thus should be widely applied.