The purpose of the study was to evaluate the feasibility of conditioning regimen with sequential chemotherapy (FLAG-IDA), followed by Fludarabine (5 days) + Busulfan (3 days) by parallel analysis of patients with refractory acute myeloid leukemia (AML) from two transplantation centers in China and France. A total of 47 refractory AML with median bone marrow blast of 35% (1-90%) and median age at 42 years (16-62) were enrolled. Thirteen patients received peripheral stem cell transplantation (HSCT) from HLA-matched sibling donor, while 18 and 16 from unrelated or haplo-identical donors, respectively. With a median follow-up of 24.3 months (1-70), 13 patients relapsed at a median time of 5.1 months (2.2-18.0) and 24 patients died due to relapse (n = 12) or non-relapsed mortality (NRM, n = 12). The estimated 3-year RR and NRM were 33.5 ± 5.7% and 25.7 ± 4.2%, respectively. The estimated 3-year overall survival (OS) and event-free survival (EFS) were 43.8 ± 7.8% and 42.3 ± 7.8%. In multivariate analysis, age (<40) and low bone marrow blast were associated with better EFS, while no difference was observed between the two centers. The patients enrolled in study were unselected, representing typical patients' population of refractory AML, and primary data demonstrated the feasibility of sequential conditioning regimen.