Background: Supra-aortic vessel reconstruction during total aortic arch replacement in acute Stanford type A aortic dissection patients with dissected distal supra-aortic vessels remains technically challenging; proximal supra-aortic vessel replacement alone carries a high risk of neurological complications secondary to intimal inversion. This study aims to evaluate clinical outcomes of self-expanding stent-assisted supra-aortic vessel reconstruction compared with proximal replacement of supra-aortic vessels alone. Methods and Results: We performed a single-center retrospective comparative analysis of 49 consecutive patients undergoing emergency total aortic arch replacement for acute Stanford type A aortic dissection from January 2022 to December 2023. Patients were divided into two groups according to intraoperative anatomy and surgeon decision: self-expanding stent-assisted supra-aortic vessel reconstruction (SAVR, n = 26) and proximal replacement of supra-aortic vessels alone (PRVA, n = 23). Neurological outcomes related to supra-aortic vessel intimal inversion, operative parameters, blood product transfusion, and short-term complications were analyzed. The mean follow-up was 18.2 ± 4.1 months (range, 12–24 months). The SAVR group exhibited significantly lower supra-aortic vessel stenosis rate (3.8% vs. 30.4%, p < 0.001) and zero cases of intimal inversion-related luminal collapse versus five cases in the PRVA group (0 vs. 5, p = 0.02). Numerically fewer cases of symptomatic stroke (0% vs. 8.7%, p = 0.09) and radiographic cerebral infarction (3.8% vs. 13.0%, p = 0.17) were observed in the SAVR group, though the differences did not achieve statistical significance. Red blood cell and fresh frozen plasma transfusion requirements, mechanical ventilation duration, and ICU stay length were significantly lower in the SAVR cohort. Cardiopulmonary bypass time and 30-day mortality were comparable between groups. Conclusions: Self-expanding stent-assisted supra-aortic vessel reconstruction represents a promising technical option during total arch replacement for acute Stanford type A aortic dissection with distal supra-aortic dissection, associated with superior branch vessel patency and favorable numerical trends in neurological and recovery-related endpoints, with a comparable early-term safety profile. Potential benefits require further validation in larger cohorts.