This study analyzed the outcomes of zygomatico-orbital fracture reconstruction using the real-time navigation system with intraoperative three-dimensional (3D) C-arm computed tomography (CT). Fifteen patients with zygomatico-orbital or isolated orbital/zygoma fractures were enrolled in this prospective cohort. For zygoma reduction, the displacement at five key sutures and the differences between preoperative and intraoperative CT images were compared. For orbital reconstruction, the bilateral orbital volume differences in the anterior, middle, and posterior angles over the medial transitional buttress were measured. Two patients required implant adjustment once after the intraoperative 3D C-arm assessment. On comparing the preoperative and postoperative findings for the zygoma, the average sum of displacement was 19.48 (range, 5.1–34.65) vs. 1.96 (0–3.95) mm (P < 0.001) and the deviation index was 13.56 (10–24.35) vs. 2.44 (0.6–4.85) (P < 0.001). For the orbit, the mean preoperative to postoperative bilateral orbital volume difference was 3.93 (0.35–10.95) vs. 1.05 (0.12–3.61) mm3 (P < 0.001). The mean difference in the bilateral angles at the transition buttress was significantly decreased postoperatively at the middle and posterior one-third. There was no significant difference in orbital volume, angle of the transition zone, and the sum of five zygoma distances between post operative results and preoperative virtual planning. The surgical navigation system with the intraoperative 3D C-arm can effectively improve the accuracy of zygomatico-orbital fracture reconstruction and decrease implant adjustment times.