<p>This study aims to evaluate the feasibility of 3D printing in percutaneous nephrolithotomy (PCNL) for the treatment of complex renal calculi. Eighty patients with complex kidney stones admitted to Guangdong Second People’s Hospital for PCNL surgery from October 1, 2021, to December 31, 2024, were randomly assigned to either the 3D printing group (40 cases) or the control group (40 cases). The 3D printing group underwent contrast-enhanced CT scanning of the urinary system. It utilized patient-specific 3D-printed models for preoperative surgical planning, simulated puncture trajectories, and patient consultations to enhance understanding of the procedure. Preoperative interview scores in the 3D printing group were significantly better than those in the control group, indicating improved patient comprehension and satisfaction. In the 3D printing group, 36 patients (90%; 95% CI: 76.9–96.0%) completed the first puncture, whereas only 20 patients (50%; 95% CI: 34.6–65.4%) in the control group did so (<i>P</i> &lt; 0.001). First-stage stone clearance was achieved in 22 patients (55%; 95% CI: 39.8–69.3%) in the 3D printing group, compared with 6 patients (15%; 95% CI: 6.2–29.5%) in the control group (<i>P</i> = 0.002). Both differences were statistically significant, demonstrating substantial improvements in surgical outcomes in this study cohort. The application of an integrated 3D printing-assisted preoperative planning strategy in PCNL for complex kidney stones was associated with higher puncture success rates and stone clearance in this study, as well as enhanced preoperative patient education. Larger multicenter studies are needed to confirm these findings.</p>