To validate the ability of the haematopoietic cell transplantation comorbidity index (HCT-CI) to predict the outcomes of patients with severe aplastic anaemia (SAA) receiving haploidentical haematopoietic stem cell transplantation (haplo-HSCT), we conducted a retrospective study including 530 SAA patients. Patients were stratified based on their HCT-CI scores into three distinct risk categories: low-risk (HCT-CI scores of 0, n = 343), intermediate-risk (HCT-CI scores of 1, n = 126), and high-risk groups (HCT-CI scores ≥ 2, n = 61). The 100-day platelet engraftment rate was significantly higher in the low-risk group compared to the intermediate-risk and high-risk groups (92.1% vs. 86.5% vs. 83.6%, P = 0.014). In addition, compared with the intermediate-risk and high-risk groups, the low-risk group demonstrated superior 5-year overall survival (OS, 91.8% vs. 83.3% vs. 70.1%, P <
0.001) and graft-versus-host disease-free/graft failure-free survival (GFFS, 80.1% vs. 71.3% vs. 63.6%, P = 0.009). Multivariate analysis revealed that elevated HCT-CI scores and previous antithymocyte globulin treatment were independent risk factors for OS, whereas elevated HCT-CI scores and donor age ≥ 40 years were correlated with worse GFFS. Consequently, the HCT-CI is associated with the clinical outcomes of SAA patients following haplo-HSCT, and it is imperative to closely monitor patients with a high comorbidity burden.