This study was aimed to explore the effect of autologous hematopoietic stem cell transplantation (auto-HSCT) and allogeneic hematopoietic stem cell transplantation (allo-HSCT) in adult patients with acute lymphoblastic leukemia and to analyze the related prognostic factors. Clinical data of 114 ALL patients receiving HSCT, including 70 auto-HSCT and 44 allo-HSCT, were retrospectively analyzed. Disease-free-survival (DFS), relapse-rate (RR) and transplantation-related-mortality (TRM) of patients receiving different HSCT were compared. The results showed that the eight-year OS and DFS in a total of 114 adult ALL patients were (40.89+/-5.27)% and (39.50+/-5.22)% respectively. The three-year DFS of ALL patients who received HSCT in phase CR1 and no CR1 were (47.63+/-5.63)% and (17.65+/-9.25)% (p=0.0034). The two-year DFS of patients who received allo-HSCT and had I/II aGVHD was (62.75+/-12.30)%, and the six-month DFS of patients who had III/IV aGVHD was 0, and the two-year DFS of patients without aGVHD was (29.35+/-9.70)% (p=0.005). The three-year DFS of patients with and without maintenance chemotherapy after transplantation were (55.12+/-7.89)% and (33.33+/-11.11)% respectively, there was significant difference between them (p=0.0499). The five-year DFS between patients received auto-HSCT and allo-HSCT in phase CR1 was not significantly different. The RR of patients received allo-HSCT was lower than that of patients received auto-HSCT, but there was no significant difference between them. The TRM of patients received allo-HSCT was higher than of patients received auto-HSCT (p=0.0313). Expression of myeloid antigen and higher LDH level in diagnosis were poor- prognostic factors. It is concluded that auto-HSCT and allo-HSCT completed in phase CR1 may improve prognosis of the patient with ALL as a method for consolidation chemotherapy, but no significant difference exists between the two HSCTs. Patients receiving allo-HSCT and having I/II aGVHD may achieve higher DFS. The maintaining chemotherapy for patients after auto-HSCT may improve therapeutic effect.