This study investigates the effects of transurethral flexible ureteroscopic lithotripsy (FURL) on renal efficacy and function in male kidney stone patients. A retrospective analysis was conducted on clinical data from 200 male patients with kidney stones treated at our hospital between February 2022 and February 2024. Depending on the technique of therapy, the patients were split into two groups: one for extracorporeal shock wave lithotripsy (ESWL) and another for FURL. Each group had 100 cases. The ESWL group was treated with ESWL, while the FURL group received FURL. The efficacy and renal function outcomes of the two methods were compared. According to the findings, the FURL group’s overall effective rate and improvement impact were considerably higher than those of the ESWL group (p < 0.05). Additionally, postoperative recovery time was shorter in the FURL group compared to the ESWL group (p < 0.05). Both groups had higher postoperative levels of blood urea nitrogen (BUN) and creatinine (Cr) than preoperative levels; however, the FURL group had lower levels of these markers than the ESWL group (p < 0.05). Additionally, the FURL group had lower postoperative white blood cell (WBC), and C-reactive protein (CRP) levels than the ESWL group (p < 0.05). Likewise, the FURL group experienced a decreased complication rate (p < 0.05). FURL treatment is valid in its expanded application due to its ability to increase efficacy, decrease complication rates, stabilize renal function indicators, and shorten recovery durations following surgery.