Objective To compare the efficacies of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the treatment of post-chronic aplastic anemia (CAA) myelodysplastic syndrome (MDS) and primary MDS. Methods A retrospective analysis was conducted on 32 patients who received allo-HSCT treatment in Department of Hematology, North China University of Science and Technology Affiliated Hospital between Feb. 2012 and Feb. 2022, including 12 patients with post-CAA MDS and 20 patients with primary MDS. The overall survival rate, cumulative incidence of relapse (CIR) rate, non-relapse mortality (NRM) rate, and event-free survival rate were compared between the 2 groups. Results The median follow-up time for CAA to progress to MDS was 120 (72-180) months. All the patients were followed up for 36 (3-79) months after allo-HSCT. The 3-year overall survival rate of the post-CAA MDS group was significantly higher than that of the primary MDS group (83.8% vs 45.0%, P＝0.035). The 3-year CIR of the post-CAA MDS group was significantly lower than that of the primary MDS group (16.7% vs 55.0%, P＝0.021). There was no significant difference in the event-free survival rates or NRM rates between the 2 groups (both P＞0.05). Conclusion The post-CAA MDS patients have better survival after allo-HSCT than the primary MDS patients. Early allo-HSCT treatment may improve the prognosis.