Background:Genetic mutations in MDS patients are closely related with clinical phenotypes and prognosis in MDS patients. But whether mutations are prognostic for outcomes after allogeneic hematopoietic stem‐cell transplantation(allo‐HSCT) remains to be elaborated.Aims:This research was done to figure out whether genetic mutations help the risk‐stratification in MDS patients received transplantation.Methods:Targeted mutational analysis were performed on samples obtained before transplantation from 151 patients underwent HSCT. Overall‐survival(OS) was calculated from the date of transplantation to date of death, and surviving patients were censored at the date on which they were last known to be alive. Diease‐free survival(DFS) was calculated from the time of transplantation to date of relapse or death and was censored at the last date known to alive without relapse. We analyzed the relationship of mutations and clinical outcomes. Curves for OS and DFS were generated using the Kaplan‐Meier method and compared using log‐rank test.Cumulative incidence of nonrelapse death and relapse was assessed using competing risks from time of HSCT to nonrelapse death or relapse by the Gray test.Results:All 151 patients carried more than one mutations, most frequently in DNAH2(47.02%), KDM6B(42.38%), USH2A(41.06%), KMT2D(38.41%), PCLO(33.11%), CCDC168(32.45%), U2AF1(29.14%), TET2(27.81%), ASXL1(25.83%), ARID1B(23.18%). In univariable analyses, TP53 or PPM1D mutations, ANKRD26 mutations, FLT3 abnormalities(including FLT3‐ITD), PDGFRB mutations were associated with shorter OS(TP53 or PPM1D, P = 0.064; ANKRD26, P = 0.025, FLT3 abnormalities: P = 0.046; PDGFRB, P = 0.044) and DFS(TP53 or PPM1D, P = 0.019; ANKRD26, P = 0.058, FLT3 abnormalities: P = 0.047; PDGFRB, P = 0.048). In multivariable analysis including clinical variables, monosomal karyotype status, HCT‐CI, and candidate genes, PDGFRB mutations and FLT3 abnormalities were each independently associated with shorter OS(PDGFRB mutations, HR = 2.979, P = 0.021; FLT3 abnormalities, HR = 2.677, P = 0.018) and DFS(PDGFRB mutations, HR = 2.779, P = 0.019; FLT3 abnormalities, HR = 2.288, P = 0.03). PDGFRB mutations(P = 0.042), ANKRD26 mutations (P = 0.004) were associated with higher non‐relapse mortality rate. FLT3 abnormalities was associated with higher relapse rate in RAEB patients(P = 0.004).Summary/Conclusion:PDGFR mutations and FLT3 abnormalities are independently associated with shorter survival in MDS patients treated with allo‐HSCT.