To evaluate the efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the conditioning of different intensities for acute leukemias of ambiguous lineage (ALAL). A total of 38 ALAL patients were treated with two conditioning of different intensities in our hospital from March 2002 to August 2010. The standard conditioning included TBI + Cy or Bu + Cy, intensified conditioning included Fludarabine + Ara-C + TBI + Cy. Cyclosporine A (CsA) and methotrexate (MTX) were administered in patients with human leukocyte antigen-matched sibling donor. And CsA, MTX plus antihuman thymocyte globulin and/or mycophenolate were used in all patients with HLA-mismatched related donor and unrelated donors transplants for graft-versus-host disease (GVHD) prophylaxis. COX regression was used to evaluate the prognostic factors of ALAL. Among 38 ALAL patients, 19 received the standard conditioning while another 19 the intensified conditioning. All patients achieved hematopoietic reconstitution. The 5-year overall survival (OS) and the disease-free survival (DFS) were 35.5% and 25.7% respectively. The 5-year OS rates were 20.2% and 48.1% (P = 0.233) and DFS 6.5% and 43.1% (P = 0.031) in the standard and intensified conditioning groups respectively. The 5-year cumulative relapsing incidence was 58.9% in all patients and 87.6% vs 30.4% in the standard and intensified conditioning groups respectively (P = 0.003). Through a COX regression model for univariate analysis, the intensified conditioning and chronic GVHD were protective factors for DFS (P = 0.001, 0.031). The intensified conditioning in ALAL patients undergoing allo-HSCT may improve the long-term patient survival and decrease the relapse of leukemia. The graft versus leukemic effect has some efficacy in ALAL patients undergoing allo-HSCT.