To evaluate the impact of transplantation timing, specifically frontline versus salvage haplo-HSCT, on the outcomes of patients with SAA. We conducted this retrospective study of 82 SAA patients who underwent haplo-HSCT following the "Beijing protocol". Patients were categorized into the frontline HSCT group (n = 40, 48.8%) and the salvage HSCT group (n = 42, 51.2%) based on transplantation timing. All 82 patients received grafts from related haploidentical donors. Multivariate analysis identified salvage HSCT (HR: 5.344, 95% CI: 1.904–14.995), ferritin levels > 1000 (HR: 5.588, 95% CI: 1.696–18.414), and CMV infection (HR: 11.909, 95% CI: 2.335–60.725) as independent risk factors for graft failure. The overall survival rate was significantly higher in the front HSCT group (90%, 36/40) compared to the salvage HSCT group (71.4%, 30/42) with mortality rates of 10.0% (4/40) and 28.6% (12/42), respectively (p = 0.029). The expected 5-year OS was significantly higher in the frontline HSCT group compared to the salvage group. Salvage HSCT, ECOG score ≥ 1, and ferritin levels > 1000 were identified as independent risk factors for prognosis. For young patients with primary SAA who lack a MSD, frontline haplo-HSCT demonstrates superior efficacy and safety, making it an effective treatment option deserving further clinical promotion.