Objective: This study aims to evaluate the clinical efficacy and short-term prognosis of using flexible cystoscopy with percutaneous nephrolithotomy to treat complex renal stones. Methods: A retrospective analysis was conducted on patients with complex kidney stones treated at Gansu Provincial Hospital of TCM and Lanzhou City No. 2 People's Hospital from July 2019 to July 2022. The study divided the patients into a control group (n=95), who underwent percutaneous nephrolithotomy alone, and an observation group (n=109), who received additional holmium laser lithotripsy and cystoscopy. We compared stone clearance rates at 5 days and 1 month post-surgery, analyzed patient prognosis over a year based on stone recurrence, and assessed risk factors through logistic regression. Perioperative data, changes in renal function indiex 3 days post-surgery, and complication rates were also evaluated. Results: The observation group exhibited a significantly higher stone clearance rate at 5 days post-surgery (P=0.002) compared to the control group, although no significant difference was observed at 1 month (P=0.823). The operative time was significantly shorter (P<0.001), and postoperative levels of BUA, Cys-c, and β2-BMG were lower (P<0.05) in the observation group. Additionally, treatment regimen, BMI, and STONE score were influencing factors for stone recurrence within 1 year. Conclusion: Flexible cystoscopy combined with percutaneous nephrolithotomy offers superior short-term outcomes in the treatment of complex renal stones, including enhanced stone clearance, reduced operative time, and minimized renal function impairment shortly after surgery. Moreover, treatment approach, BMI, and STONE score play pivotal roles in predicting stone recurrence.