We present here the three-dimensional (3D) visualization fused with ultrasound and to evaluate its clinical application effect preliminarily. One hundred and eighteen patients with renal calculi in our hospital from September 2017 to December 2019 were prospectively randomized into two groups. The experimental group was treated with percutaneous renal puncture guided by the 3D visualization fused with ultrasound. The control group was treated with percutaneous renal puncture guided by B-ultrasonography (B-US). The puncture time in the experimental versus control group was 4.36 ± 1.28 min versus 10.72 ± 2.94 min (P = 0.000), operation time was 65.85 ± 10.63 min versus 81.34 ± 12.52 min (P = 0.000), and the loss of hemoglobin was 8.55 ± 3.76 g/L min versus 13.33 ± 5.81 g/L(P = 0.000), and the success rate of establishing the channel at one time was 98.41% versus 81.82% (P = 0.002), and the coincidence rate between the channel and the longitudinal axis of the target renal calyx was 88.89% versus 60.00% (P = 0.000). The 3D visualization fused with ultrasound could guide precise puncture to target calyces, reduce operation time, bleeding, and difficulty of puncture.