<p>Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the most effective salvage strategy for B-cell acute lymphoblastic leukemia (B-ALL). In this study, we explored the efficacy and safety of cladribine and medium-dose cytarabine intensified busulfan plus cyclophosphamide conditioning regimen (CBAC) for high-risk B-ALL patients at complete remission (CR) after chemotherapy undergoing allo-HSCT. And compared it with patients historical received traditional total body irradiation plus cyclophosphamide (TBI-Cy) regimen. The 3-year non-relapse mortality (NRM), cumulative incidence of relapse (CIR), disease-free survival (DFS) and overall survival (OS) of CBAC and TBI-Cy group were 15.0% vs. 11.1% (<i>p</i> = 0.576), 17.3% vs. 35.7% (<i>p</i> = 0.077), 67.7% vs. 53.2% (<i>p</i> = 0.235) and 74.3% vs. 66.8% (<i>p</i> = 0.482). Overall cohort multivariate analysis indicated TBI-Cy increased the risk of relapse after transplantation compared with CBAC (HR: 2.544, <i>p</i> = 0.049). Subgroup analysis revealed that among cytogenetic high-risk patients, the CBAC group showed a trend of higher 3-year DFS (75.1% vs 52.6%, <i>p</i> = 0.073). Among patients with minimal residual disease positive (MRD⁺) at transplantation, the CBAC group showed higher 3-year DFS (60.0% vs 11.1%, <i>p</i> = 0.018). In conclusion, CBAC conditioning regimen may reduce relapse without increasing NRM, improving the prognosis of high-risk B-ALL patients, especially those with cytogenetic high-risk factors or MRD⁺ at transplantation.</p>