Objective: To compare the efficacy of new percutaneous technique (“ultra-mini PCNL”, UMP), shock wave lithotripsy (SWL) and flexible ureteroscopy (FURS) on the treatment of 1–2 cm lower pole kidney stones, and to determine the advantages and disadvantages of each method. Materials and Methods: This prospective study was based on data collected from the files of patients between March 2015 and March 2017. This study recruited a total of 180 patients with single radio-opaque lower caliceal calculi of 1–2 cm. All patients were randomly divided into 3 groups: group A was treated with UMP, group B was treated with FURS by using holmium laser and group C was treated with SWL by using the electromagnetic lithotripter. The average age, sex, size of the stone, the time of operation, the rate of no stone, the time of hospitalization, the rate of retreatment, the cost and the complications of the 3 groups were compared. The success of the operation was defined as no residual stone or < 0.3 cm on computed tomography at 3 months postoperatively. Results: The stone burdens of the groups were equivalent. The re-treatment rate in group C was significantly higher than that in group A and B (30 vs. 1.6%, 5%). The average operating time in group B (93.35 ± 21.64 min) was statistically significantly longer than that in group A and C (68.58 ± 15.82 min, 46.33 ± 5.81 min). Although the time of hospitalization of group A (5.32 ± 1.20 day) was longer than that of group B (3.22 ± 0.52 day) and C (1.08 ± 0.28 day; p < 0.05). The stone-free rate (SFR) in UMP, FURS, SWL were 98, 92, and 73% respectively; the highest SFR was in the UMP group (p < 0.05). The complication rates were evaluated by using the Clavien grading system, which were determined to be 16.67% in UMP, 6.67% in SWL and 8.33% in FURS. In particular, the complications of GI and GII were more common in group A (p < 0.05). Conclusions: UMP, FURS, and SWL are all safe and effective in the treatment of 1–2 cm lower pole kidney stones. UMP and FURS had a better SFR than SWL, but the time of hospitalization in UMP group was longer and there were more complications in the UMP group. In addition, the operation time of FURS is longer as compared to UMP and SWL, and there is a higher rate of postoperative fever. The invasiveness and cost of SWL were lower than that of UMP and FURS, but the re-treatment rate was higher.