BACKGROUND This retrospective study aimed to compare outcomes from super-mini percutaneous nephrolithotomy (SMP) combined with flexible ureteroscopic lithotripsy (FURL) and FURL alone in 205 patients with 2.5-4.2 cm diameter complex kidney stones. MATERIAL AND METHODS Between January 2018 and December 2022, 92 patients were treated with SMP combined with FURL (group A), and 113 patients were treated with FURL alone (group B). The stone-free rate (SFR), retreatment ratio, operation time, mean decline in hemoglobin level, postoperative pain visual analogue scale (VAS), and postoperative hospitalization time and complications were analyzed and compared between the 2 groups. RESULTS The SFR 3 days after the operation was 85.87% in group A, which was significantly higher than that in group B (72.57%) (P=0.021). The rate of retreatment in group A (3.26%) was significantly lower than that in group B (10.62%) (P=0.044). The SFR after 90 days was higher in group A (94.57%) than in group B (90.27%) (P=0.254). The mean decrease in hemoglobin, postoperative hospitalization duration, and VAS score 6 hours after the operation were all significantly higher in group A than in group B (P<0.05). However, there was no significant difference in operation time, VAS score at 12 and 24 hours after the operation, and complication rate. CONCLUSIONS In the treatment of complex renal stones, compared with FURL, SMP combined with FURL in the oblique supine lithotomy position has the advantages of a higher early SFR with no increased risk of complications.