A novel conditioning regimen using helical tomotherapy (HT) was developed to deliver 10 Gy for total body irradiation (TBI) and simultaneously augment dose to 12 Gy for targeted dose boost to total marrow, central nervous system leukemia, and extramedullary disease sites in patients with high-risk or relapsed/refractory acute lymphoblastic leukemia (ALL) receiving haploidentical allogeneic hematopoietic stem cell transplantation (allo-HSCT). Fourteen patients were included, eight of these patients were in first complete remission (CR1), one was in CR2, one had a partial response and four patients had refractory disease at transplantation. The median delivered average dose was 11.395 Gy (range 10.06-12.17). The median planning target volume D95 was 8.2 Gy (range 7.52-9.01). The median delivered dose to skeleton bone with active bone marrow sites was 12.685 Gy (range 11.12-13.52). The results of this trial suggest that using HT TBI confers satisfactory immunosuppression and excellent eradication of malignant cells in patients with high-risk ALL undergoing allo-HSCT, especially in those with refractory ALL. After a median follow-up of 14.6 months (range 4-28), four patients experienced non-relapse mortality, ten patients are alive in durable CR including remission of extramedullary leukemic infiltration. One-year overall survival and disease-free survival rates post-transplantation were both 70.7%.