Objective. To research the application of CTU-assisted Doppler ultrasound puncture in uncatheterized PCNL, its influence on patients’ complications, and its clinical value in a case-control study. Methods. One hundred and forty-four patients who went through percutaneous nephrolithotomy (PCNL) from March 2019 to June 2021 in our hospital were arbitrarily assigned into the CTU group (
n
=
72
) and CT plain scan group (
n
=
72
). CTA+CTU was adopted to determine the puncture passage in the CTU group, and CT scan was employed in the CT group. The intraoperative blood loss, postoperative blood loss, operation time, hospital stay, primary stone removal rate, and the incidence of intraoperative and postoperative complications were compared. The visual analogue score (VAS) was employed to assess the degree of postoperative wound pain. Results. The first-stage stone removal rate in the CTU group was 95.83% (69/72), which was remarkably higher compared to the CT plain scan group, which was 81.94% (59/72), and the difference was statistically significant (
P
<
0.05
). The overall rates of intraoperative complications were 6.94% (5/72) in the CTU group and 18.06% (13/72) in the CT plain scan group, respectively, which exhibited great differences (
P
<
0.05
). In addition, the overall rates of intraoperative complications were 2.78% (2/72) in the CTU and 13.89% (10/72) in the CT plain scan group, respectively, and the difference was statistically significant (
P
<
0.05
). The operation time and postoperative hospital stays in the CTU group were remarkably shorter compared to the CT group, and the difference was statistically significant (
P
<
0.05
). The intraoperative and postoperative blood loss of CTU group displayed obvious less than that of the CT group, and the difference was statistically significant (
P
<
0.05
). The VAS were compared 24 hours after surgery. After operation, the VAS of 24 hours after operation in the CTU group (
0.92
±
0.12
) were remarkably lower compared to the CT group (
1.22
±
0.15
), and the difference was statistically significant (
P
<
0.05
). Discussion. PCNL is constantly being optimized by CTU-assisted Doppler ultrasound puncture to improve stone clearance rates, reduce postoperative bleeding, be less painful, provide rapid recovery, and provide safe and feasible results. It is therefore worthwhile to standardize and then widely promote it in clinical practice.