<p>Acute myeloid leukemia (AML) is the most common type of acute leukemia, of which relapsed/refractory AML (R/R AML) is the major cause of death in these patients. Allogeneic hematopoietic stem cell transplantation (allo<b>-</b>HSCT) remains to be the mainstay curative treatment for patients with R/R AML. However, the prognosis of R/R AML is still unsatisfactory. Systematic analysis of the clinical-biological management and characteristics throughout the HSCT process in R/R AML patients may break through the current predicament of poor prognosis. This review provides a holistic analysis of the complete clinical management process for R/R AML, from disease mechanisms to post-transplantation therapies. Novel conditioning and post-transplantation regimens incorporating target/immune-based therapies have improved outcomes of HSCT in R/R AML patients. The widespread adoption of haploidentical transplantation has ended the era of donor scarcity, while donor switching remain a critical clinical outcome for patients with second-transplantation. This study provides guidance for clinical decision-making, though further optimization of prognostic models and integration of novel biomarkers are needed to advance personalized treatment strategies for R/R AML patients in the future.</p>