Objective To investigate the clinical efficacy of super-mini-percutaneous nephrolithotripsy with short combined rigid endoscope for the treatment of lower calyceal calculus. Methods Patients with lower renal caliceal calculus admitted to the Third Affiliated Hospital of Guangxi Medical University from June 2020 to August 2023 were selected. According to the random number method, patients were divided into percutaneous nephrolithotomy group and flexible ureteroscopy group, with 50 cases in each group. The percutaneous nephrolithotomy group carried out super-mini-percutaneous nephrolithotripsy with a short combined rigid endoscope and a negative-pressure stone clearance system. The flexible ureteroscope group underwent transurethral retrograde flexible ureteroscopic lithotripsy. The clinical efficacy and safety indicators of the two groups of patients were evaluated. Results Some cases were excluded due to intraoperative factors. Eventually, 47 patients were included in the percutaneous nephrolithotomy group and 44 in the flexible ureteroscopy group. Compared with the flexible ureteroscopy group, the percutaneous nephrolithotomy group had shorter operation time, higher stone clearance rate before discharge and 1 month after operation, and all these differences were statistically significant (all P<0.05). The postoperative serum procalcitonin and C-reactive protein levels in the percutaneous nephrolithotom group were both lower than those in the flexible ureteroscopy group, with all these differences being statistically significant (all P<0.05). There were no statistically significant differences between the two groups in terms of hemoglobin level, white blood cell count, and the incidence of postoperative complications (all P>0.05). Conclusions The application of super-mini-percutaneous nephrolithotripsy with a short combined rigid endoscope and a negative-pressure stone clearance system for the treatment of lower calyceal calculus offers advantages such as a short operation time, a high stone clearance rate, and good postoperative safety. Therefore, it is worthy of further clinical promotion and application.