Objective A case-control study was conducted to compare the efficacy and prognostic factors of flexible ureteroscopic lithotripsy (FURL) and percutaneous nephrolithotomy (PCNL) when treating complex upper urinary tract renal calculi based on a retrospective cohort study. Methods The study period was from October 2019 to December 2021. A retrospective study was carried out on 100 patients with complicated upper urinary tract nephrolithiasis who underwent surgery in the Urology Department of our hospital. They were assigned into two groups: FURL and PCNL groups. The intraoperative blood loss, operation time, hematuria duration, hospital stay, primary stone removal rate, incidence of intraoperative and postoperative complications, VAS score, level of inflammatory factors, and micturition function were compared. According to the postoperative prognosis, the patients were reassigned into two groups: good prognosis group (n = 38) and poor prognosis group (n = 106). The factors related to poor prognosis after FURL and PCNL were screened, and multivariate loglistic regression analysis was adopted to determine the risk factors. Results The primary stone clearance rate in the PCNL group was significantly higher than that in the FURL group, and there was no significant difference in the incidence of intraoperative and postoperative complications between the two groups (P > 0.05). The intraoperative blood loss and the duration of hematuria in the PCNL group were significantly shorter than those in the FURL group, and the operation time and postoperative hospital stay in the FURL group were longer than those in the FURL group. The postoperative VAS score in the study group was significantly lower than that in the control group (P < 0.05). The levels of CRP, IL-1, TNF-α, and NF-κB in both groups decreased after operation, and the level of inflammatory factors in the PCNL group was significantly lower than that in the FURL group (P < 0.05). The indexes of IPSS and Qmax in the PCNL group were significantly lower than those in the control group 3 months after operation. The index of micturition function in the PCNL group was significantly lower than that in the FURL group. Preoperative use of immunosuppressant, preoperative stone fever, positive preoperative urine culture, preoperative urinary leukocyte count ≥ 544 × L, intraoperative urinary opacity, and pus fur were significantly correlated with poor prognosis of ureteral patients (P < 0.05). Preoperative stone fever, high preoperative urinary leukocyte count, intraoperative urinary turbidity, and suppurative fur were independent risk factors for postoperative SIRS in patients with ureteral calculi. Conclusion PCNL is effective when treating complex upper urinary tract renal calculi. Compared with FURL, PCNL can remarkably reduce intraoperative blood loss and hematuria duration, can enhance micturition function, and will not remarkably increase the incidence of intraoperative and postoperative complications, high safety. High white blood cell count in urine before operation, fever due to stone before operation, turbid urine, and purulent fur during operation are independent risk factors for postoperative adverse outcome in patients with complex upper urinary tract renal calculi. Patients should be fully treated before surgery.