To report the outcomes and determine the effectiveness of a comprehensive organ protection strategy in total arch replacement. A total of 350 patients who underwent total arch replacement were enrolled. 54 patients underwent the comprehensive organ protection strategy with bilateral antegrade cerebral perfusion (bACP) and aortic balloon occlusion (ABO) technique (comprehensive strategy group) and 296 patients underwent the standard strategy with unilateral antegrade cerebral perfusion (standard strategy group). Inverse probability of treatment weighting (IPTW) was used to balance the baseline characteristics. After IPTW, the comprehensive strategy group had lower incidences of 30-day mortality (0.9% vs 4.9%, P = 0.002), continuous renal replacement therapy (CRRT) (0.6% vs 10.3%, P < 0.001), renal failure (4.6% vs 13.7%, P < 0.001), hepatic dysfunction (11.6% vs 21.1%, P = 0.001), and shorter duration of mechanical ventilation [16 (13, 31) vs 20 (14, 48) hours, P = 0.011]. Multivariable logistic analysis showed the comprehensive strategy was an independent protective factor of 30-day mortality (odds ratio (OR): 0.242, 95% confidence interval (CI): 0.068-0.867, P = 0.029), CRRT (OR: 0.045, 95% CI: 0.008-0.264, P = 0.001), renal failure (OR: 0.351, 95% CI: 0.156-0.788, P = 0.011), and mechanical ventilation >20 hours (OR: 0.531, 95% CI: 0.319-0.883, P = 0.015). Kaplan-Meier analysis showed mid-term survival was comparable. The comprehensive organ protection strategy might improve early survival, reduce the use of CRRT, have protective effects on the kidney, and shorten mechanical ventilation time in total arch replacement. This strategy might be considered a viable alternative in total arch replacement.