Objective: To explore the prognostic factors of patients undergoing allogeneic hematopoietic stem cell transplantation and treatment of cytarabine combined with fludarabine. Methods: The data of 174 patients who received allogeneic hematopoietic stem cell transplantation in the hospital from March 2014 to August 2017 were retrospectively analyzed. Patients receiving pre-treatment of cytarabine combined with fludarabine, and pre-treatment of cytarabine combined with daunorubicin were included in the study group (n=94) and the control group (n=80). Therapeutic effects, adverse reactions, and prognosis of the two groups were compared, and the prognostic factors of study group were analyzed. Results: The total effective rate of pre-treatment in the study group was significantly higher than that in the control group (89.36% vs 76.25%, P<0.05). The incidence of bone marrow suppression in the study group was significantly higher than that in the control group (P<0.05). There were no statistically significant differences in the incidences of adverse reactions such as graft-versus-host disease, mucosal injury, liver injury, infection, and cardiotoxicity (P>0.05). The 3-year overall survival rate and recurrence-free survival rate in the study group were higher than those in the control group (80.9% vs 55.0%, 89.2 % vs 75.0%, log-rank χ²=13.790, 6.278, P<0.05). The results of univariate analysis and multivariate COX regression analysis showed that complete remission during transplantation, acute and chronic graft-versus-host disease were independent influencing factors of recurrence (P<0.05). Age ≥35 years old, complete match results, and complete remission of disease during transplantation were independent influencing factors for survival (P<0.05). Conclusion: Cytarabine combined with fludarabine is an effective pre-treatment plan for patients undergoing allogeneic hematopoietic stem cell transplantation. The prognosis of patients is affected by various factors such as remission and acute graft-versus-host disease.