[Objective] To explore the efficacy and safety of retrograde intrarenal surgery (RIRS) using a flexible negative pressure suction sheath in the treatment of upper urinary tract stones >2 cm in diameter, to provide reference for the diagnosis and treatment of such disease. [Methods] Clinical data of 155 patients who underwent surgery for upper urinary tract stones during Nov.2022 and Nov.2023 at the Second Affiliated Hospital of Shaanxi University of Chinese Medicine were retrospectively analyzed.The patients were divided into 3 groups: percutaneous nephrolithotripsy (PCNL) group (n=54), conventional sheath RIRS group (n=41), and flexible sheath RIRS group (n=60). The general and clinical data of the 3 groups were compared. [Results] The PCNL group had more patients with severe hydronephrosis (22.22% vs. 4.88%, 5.00%, P=0.027) and smaller IPA involving the lower calyx [(36.17±17.6)° vs. (48.57±17.56)°, (47.41±10.82)°, P=0.014] than the conventional sheath RIRS group and flexible sheath RIRS group.Three days after operation, the stone-free rate (SFR) was 90.74%, 53.66% and 78.33% in the PCNL, conventional sheath RIRS, and flexible sheath RIRS groups, respectively (P<0.05). At 1 month postoperatively, the SFR was 92.59%, 73.17%, and 81.67%, with no statistically significant difference between the PCNL and flexible sheath RIRS groups (P>0.05), but was higher than that in the conventional sheath RIRS group (P<0.05). The PCNL group had shorter operation time than the two RIRS groups [(65.22±17.67) min vs. (91.73±20.57) min, (94.38±24.75) min, P<0.001], longer postoperative hospital stay [(5.0(4.0, 7.0) d vs.3.0(2.0, 4.0) d, 3.0(2.0, 4.0) d, P<0.001], greater decrease in hemoglobin level [(18.00±5.78) g/L vs. (5.57±5.16) g/L, (7.42±5.09) g/L, P<0.001], and higher visual analogue scale (VAS) score [(4.83±1.48) min vs. (2.95±1.07) min, (3.05±1.21) min, P<0.001], while there was no difference between the two RIRS groups (P>0.05). The costs were lower in the flexible sheath RIRS group than in the conventional sheath RIRS group but higher than in the PCNL group [(23 311.19±1 341.20)yuan vs.(24 550.49±1 172.51)yuan, (15 351.97±1 101.4)yuan, P<0.001]. The overall incidence of complications was similar among the three groups, but stone street occurred only in the conventional sheath RIRS group. [Conclusion] For the treatment of patients with upper urinary tract stones >2 cm, RIRS has shorter postoperative hospital stay, lower hemoglobin decrease, and lower VAS score compared to PCNL; the early postoperative SFR of flexible sheath RIRS is superior to that of conventional sheath RIRS, and the 1-month SFR is comparable to that of PCNL, with a low incidence of stone street.