The most effective post-first CR1 treatment for patients with AML, allogenic hematopoietic SCT (allo-HSCT) or autologous hematopoietic SCT (HSCT), remains to be conclusively determined. This study aimed to compare the effectiveness of treatment with allo-HSCT or auto-HSCT in patients with AML after CR1. We retrospectively reviewed medical records of 127 patients with AML who received allo- (n=52) or auto-HSCT (n=75) after achieving CR1 at a single medical center. The disease-free and overall survival rates and complications were analyzed. During a median follow-up of 1215 days, all patients (100%) in allo-HSCT group and 94.7% of patients in the auto-HSCT group had successful outcomes. The disease-free survival rates were 65.3% and 50.6% for allo- and auto-HSCT groups, respectively (P=0.158), while the overall survival rates were 65.3% and 54.9%, respectively (P=0.486). The recurrence rate was higher with auto-HSCT, whereas the GVHD only happened with allo-HSCT. In conclusion, auto-HSCT was as effective as allo-HSCT for the treatment of patients with AML after CR1. This is encouraging given that allo-HSCT is not always feasible in China because of a lack of matching donors.