Iliosacral screw insertion by computer-assisted navigation gradually became the main technique in some hospitals, but the expensive price limited the extensive application. But other techniques such as 3D printed template was used to place iliosacral screw as novel method. This study was to compare the efficiency of percutaneous iliosacral screw placement by using patient-specific template and computer-assisted navigation. Total of 58 patients from September 2017 to September 2021 with sacral injury were treated operatively with percutaneous screw technique, which was selected for this retrospective analysis and divided into two groups (template and computer-assisted navigation). There were 31 patients in template group and 27 patients in computer-assisted navigation group. The surgical details (operation time, blood loss, number of screw placements, and number of fluoroscopies), complications, radiographic and clinical results were recorded. The quality of reduction was assessed by the Matta scoring system. T-test and rank-sum test was used in this study. Operation time in template group was less (33.97 ± 16.61 < 60.31 ± 11.46 min, p < 0.01), but the preoperative preparation time was more (6.35 ± 1.60 > 5.41 ± 1.58, p < 0.05). The quality of reduction in both groups was no difference (p = 0.352). A patient was complicated with gluteal vessel injury in operation in navigation group, which was treated with ligation, but the same injury was not observed in template group. The related surgical data of patient with gluteal injury was ignored in statistical analysis. Both of the two techniques could improve surgical efficiency, the operation time in template was less than computer-assisted navigation group, but the preoperative preparation time was more.