In recent years, great progress has been made in haploidentical hematopoietic stem cell transplantation (haplo-HSCT) treatment for hematological malignant diseases because of the advent of novel conditioning regimens, optimized graft manipulation, improved graft-versus-host disease (GVHD) prophylaxis, and advances in supportive care. Recent studies have shown very favorable outcomes in severe aplastic anemia (SAA) patients, with comparable outcomes to those of patients receiving immune suppressive therapy (IST) and allogeneic HSCT from a matched sibling donor (MSD) or matched unrelated donor (MUD). However, most of the previous studies relied on single-center data analyses, and the conditioning regimen, GVHD prophylaxis and supportive care used were relatively singular. We do not know whether there are differences in the survival of SAA patients after haplo-HSCT and MSD-HSCT under conditions involving different transplant centers, conditioning regimens and GVHD prophylaxis. This is a disease-specific, multicenter and retrospective study. We retrospectively studied 156 consecutive patients with SAA who underwent haplo-HSCT or MSD-HSCT at four transplant centers in China. The 5-year overall survival (OS) rate was 87.5% in the haplo-HSCT group and 89.7% in the MSD-HSCT group. The time to hematopoietic reconstitution, incidence of graft versus host disease, and infection and graft failure rates were not significantly different between the groups. Haplo-HSCT achieved outcomes comparable to those of MSD-HSCT for SAA patients. According to the nomogram score, we developed a SAA prognostic scoring system. Haplo-HSCT should be considered an effective alternative for patients with SAA without a matched sibling donor. The SAA transplant-specific prognostic scoring system proposed in this study can conveniently predict the OS for SAA patients following MSD-HSCT or haplo-HSCT.