To compare the efficacy and postoperative infection rate of super mini percutaneous nephrolithotomy(SMP) and flexible ureteroscopic lithotripsy(FURL) in patients with diabetic nephrolithiasis, and to explore the risk factors associated with postoperative infection following these two procedures. The medical history and surgery details of 252 patients with diabetic nephrolithiasis who underwent lithotripsy in our hospital between January 2018 and May 2023, including 144 SMP and 108 FURL, were reviewed and compared. Perioperative outcomes were compared between the two groups. Logistic regression was performed to identify the significant risk factors for infection after each procedure(SMP and FURL). SMP achieved a higher stone-free rate (SFR) on postoperative day 1(POD-1) and postoperative day 30(POD-30) compared to FURL(p<0.05). The mean operative time was shorter in SMP (p<0.01). FURL was associated with less hemoglobin drop (p<0.01) and shorter length of stay (p<0.01). The incident rate of systemic inflammatory response syndrome(SIRS) was higher after SMP (p=0.019), while the incident rate of urinary tract infection(UTI) was higher after FURL (p=0.021). Overall postoperative infection and sepsis rates were similar between the two procedures. Logistic regression analysis revealed that gender (OR: 0.225, 95% CI: 0.079-0.639), HbA1c (OR: 3.516, 95% CI: 1.841-6.716), and operation time (OR: 1.037, 95% CI: 1.008-1.066) were independent risk factors for infection after FURL, while operation time (OR: 1.063, 95% CI: 1.022-1.106) and HbA1c (OR: 7.443, 95% CI: 2.956-18.742) significantly predicted SMP-associated infections. In diabetic patients, SMP demonstrated higher SFR and shorter operation time, while FURL was associated with less bleeding and shorter hospitalization. SMP had a higher incident rate of SIRS and FURL had a higher incident rate of UTI. Elevated HbA1c and prolonged operative duration increased infection risk after both procedures, while male gender was an additional risk factor for FURL-related infections.