To investigate the effect of retrograde intrarenal surgery (RIRS) and percutaneous nephrolithotripsy on the inflammatory reaction, renal function indicators and clinical efficacy in male patients with kidney stones. 122 male patients with kidney stones were separated into the study group (n = 61) and the control group (n = 61) in terms of distinct clinical treatment regimens. The study group was treated with retrograde intrarenal surgery, while the control group was treated with percutaneous nephrolithotripsy. Inflammatory reaction indicators (Interleukin-6 (IL-6), Interleukin-10 (IL-10), serum tumor necrosis factor-α (TNF-α)), renal function indicators (blood urea nitrogen (BUN), serum creatinine (Scr), blood uric acid (BUA), serum β2 microglobulin (BMG)) and other clinical indicators (operative time, hospital stay, intraoperative blood loss, Visual analogue scale (VAS) pain score, complications) were observed and compared. Upon the treatment, significantly lowered inflammatory factors including IL-6, IL-10, TNF-α and renal function indicators including BUN, Scr, BUA, BMG were shown in study group. Notably shortened operative time and hospital stay were presented in study group with lowered intraoperative blood loss and pain score. The total incidence of complications in study group was 3.28%, significantly lower than 14.75% in control group. Compared with percutaneous nephrolithotripsy, retrograde intrarenal surgery for the treatment of male kidney stones with a diameter of less than 3 cm can improve the inflammatory reaction of male patients, maximize the preservation of renal function indicators, and eminently promote the clinical comprehensive efficacy.