Objective To investigate the clinical efficacy of flexible ureteroscopic holmium laser lithotripsy （FURL） in the treatment of kidney stones, and to compare it with percutaneous nephrolithotripsy （PCNL）. Methods A total of 68 patients with kidney stones admitted from January 2022 to December 2023 were selected as study subjects, and were divided into FURL group and PCNL group according to the operation type, with 34 cases in each group. The efficacy of the two groups was compared. Results The total clinical effective rate of the FURL group was significantly higher than that of the PCNL group （P<0.05）. The operation time of the two groups was not different （P>0.05）. The amount of intraoperative blood loss and hospital stay in the FURL group were significantly lower than those in the PCNL group （P<0.05）. Before operation, the renal function indexes of the two groups were not different （P>0.05）. After 3 d of operation, the renal function indexes in both groups were significantly increased （P<0.05）, but the indexes in the FURL group were lower than those in the PCNL group （P<0.05）. The incidence of postoperative complications in the FURL group was significantly lower than that in the PCNL group （P<0.05）. Conclusion Compared with PCNL, FURL is more effective in treating kidney stones, effectively improves renal function, facilitates postoperative rehabilitation, and has fewer complications.