It was commonly accepted that adverse-risk acute myeloid leukemia patients should receive allogeneic hematopoietic stem cell transplantation (allo-HSCT) in first complete remission (CR1). In this multicenter study, we aimed to compare the post-transplant outcomes between patients receiving venetoclax with azacitidine (VEN-AZA, n = 47) and intensive chemotherapy (IC, n = 264) before allo-HSCT. In total cohort, the 3-year probabilities of overall survival, leukemia-free survival, and event-free survival of IC group were all better than VEN-AZA group, particularly for the patients with ASXL1 mutation or with SF3B1 mutation. Even in the patients ≥ 55 years or those with HCT-CI ≥ 1 scores before allo-HSCT, the survival of VEN-AZA group was not superior to the IC group. After propensity score matching, the overall survival at 1 year after allo-HSCT for IC group was better than that of VEN-AZA group (93.6 vs. 78.0%, P = 0.034), and the other clinical outcomes were comparable between VEN-AZA and IC groups. TP53 mutation was the most important adverse prognostic factor for post-transplant relapse and survival. Thus, our results did not support the preferential use of VEN-AZA over IC regimens in young and medical fit adverse-risk AML patients who would receive allo-HSCT in CR1.