SummaryAllogeneic haematopoietic stem cell transplantation (HCT) is the curative treatment for myelodysplastic syndrome with a complex karyotype (CK‐MDS). However, only a few studies have been limited to patients with CK‐MDS undergoing allogeneic HCT. This study aimed to identify the risk factors for patients with CK‐MDS undergoing allogeneic HCT. We included 691 patients with CK‐MDS who received their first allogeneic HCT. The overall survival (OS) was the primary end‐point, estimated using the Kaplan–Meier method. Prognostic factors were identified using a Cox proportional hazards model. The 3‐year OS was 29.8% (95% confidence interval [CI]: 26.3–33.3). In the multivariable analysis, older age (hazard ratio [HR]: 1.44, 95% CI: 1.11–1.88), male sex (HR: 1.38, 95% CI: 1.11–1.71), poor haematopoietic cell transplant comorbidity index (HR: 1.47, 95% CI: 1.20–1.81), red blood cell transfusion requirement (HR: 1.58, 95% CI: 1.13–2.20), platelet transfusion requirement (HR: 1.85, 95% CI: 1.46–2.35), not‐complete remission (HR: 1.55, 95% CI: 1.16–2.06), a high number of karyotype abnormality (HR: 1.63, 95% CI: 1.18–2.25) and monosomal karyotype (HR: 1.49, 95% CI: 1.05–2.12) were significantly associated with OS. Thus, the 3‐year OS of allogeneic HCT was 29.8% in patients with CK‐MDS, and we identified risk factors associated with poor OS.