To investigate the efficacy of super-mini-PCNL (SMP) and ureteroscopy in kidney stone (KS) sufferers and learn the risk factors of postoperative infection. A retrospective analysis was performed on 180 KS sufferers who were diagnosed and treated in our hospital from May 2019 to May 2021. They were enrolled into an observation group (OG, n = 104) and a control group (CG, n = 76) based on different treatment methods. Therein, the former was treated with SMP, while the latter was treated with ureteroscopy. The operation time, blood loss, hospital stay, recent stone-free rate (one week after operation), changes of serum creatinine (SCr), blood urea nitrogen (BUN), and cystatin C (CysC) levels before and after operation and complications were compared. Those sufferers were assigned to infected and uninfected groups based on their postoperative infection. The risk factors were assessed through logistic regression, and the model formula was established. The predictive value of this model for infection was tested through RO. Compared with CG, the operation time of the OG was longer, the blood loss and hospital stay were lower ( P < 0.05), and the stone-free rate was higher ( P < 0.05). Renal function indexes before and after treatment ( P > 0.05) and postoperative complications revealed no significant difference ( P > 0.05). Logistic regression analysis manifested that preoperative urinary tract infection (OR: 4.690, 95% CI: 1.170–18.802), preoperative blood glucose level (OR: 11.188, 95% CI: 2.106–59.442), positive urine culture (OR: 10.931, 95% CI: 2.453–48.705), and infectious stones (OR: 3.951, 95% CI: 1.020–15.300) were independently related to infection. The risk prediction equation is logit( p )=−8.913+1.545 × X 1+2.415 × X 2+2.392 × X 3+1.374 × X 4, with a goodness-of-fit value of 0.545. The AUC is 0.930, so SMP is superior to ureteroscopy in KS sufferers. Preoperative urinary tract infection, preoperative blood glucose level, positive urine culture, and infectious stones are independently related to infection.