Fludarabine and a myeloablative dose of busulfan (Flu/Bu4) can improve prognosis after allogeneic hematopoietic stem cell transplantation (HSCT) with melphalan (Mel). We investigated the prognostic impact of adding Mel to Flu/Bu4 by comparing between Flu/Bu4/Mel and Flu/Bu4 groups. This study included 846 propensity score (PS)-matched patients who received either Flu/Bu4/Mel (n = 423) or Flu/Bu4 (n = 423) from 2394 patients enrolled in a multicenter prospective registry, from January 2010 to December 2016. The primary endpoint (5-year overall survival [OS]), and the prognostic impact of adding Mel was evaluated using Cox regression analysis. The study population median age was 58 (interquartile 50-64) years and 61.0% were male. Patient characteristics were well-balanced between groups. Five-year OS was 34.2% (95% confidence interval [CI]: 27.3-41.1%) and 30.1% (24.8-35.6%) in the Flu/Bu4/Mel and Flu/Bu4 groups, respectively (log-rank P = 0.019). The adjusted hazard ratio of adding Mel was 0.77 (95% CI: 0.62-0.96) (P = 0.022) for the 5-year OS, and this attributed to a lower incidence of 5-year relapse (0.71, 0.56-0.90, P = 0.005) and relapse associated mortality (0.73, 0.57-0.95, P = 0.018). There was no statistical difference in 5-year non-relapse mortality between groups (log-rank P = 0.855). Flu/Bu4/Mel was associated with better 5-year OS compared to Flu/Bu4 in a PS-matched cohort after allogeneic HSCT.