A novel reduced-toxicity conditioning (RTC) regimen of busulfan, fludarabine, cyclophosphamide, and antithymocyte globulin (Bu/Flu/Cy/ATG) followed by haploidentical hematopoietic stem cell transplantation (haplo-HSCT) in older patients with hematologic malignancies has been reported and the results was encouraging. However, the safety and efficacy of this regimen was unknown in older myelodysplastic neoplasms (MDS) patients. From January 2018 to December 2021, 68 consecutive older patients (aged over 50) using the RTC regimen for T-cell replete haplo-HSCT (RTC group) at our center were eligible, 68 patients aged under 50 using modified busulfan, cyclophosphamide plus antithymocyte globulin regimen (Bu/Cy/ATG) (Bu/Cy/ATG group) were randomly selected from 223 MDS patients during the same period in a 1:1 ratio matched-pair analysis for patient sex, World Health Organization (WHO) category, international prognostic scoring system (IPSS) risk group, time from diagnosis to HSCT, chemotherapy in advanced, response after chemotherapy, donor sex, infused mononuclear cells and the CD34-positive cell count. The transplant outcomes were also compared between the RTC group and the matched sibling donor (MSD) haploidentical stem cell transplantation (HSCT) with the busulfan and cyclophosphamide (Bu/Cy) conditioning regimen. The cumulative incidences of grade II-IV acute graft versus host disease (aGVHD) in the RTC group were significantly lower than that in the Bu/Cy/ATG group. The 3-year cumulative incidences of treatment related mortality (TRM) in the two groups were 12.3% versus 14.7% (P=0.613). The cumulative incidences of relapse, disease-free survival (DFS) and overall survival (OS) were comparable between the two groups. The outcomes were better in RTC group than those patients received MSD transplant, with lower incidence of TRM, and higher OS and DFS. The advantages were still significant when comparing patients receiving children donors HSCT in RTC group with MSD transplant in survival and TRM. Children donor with the RTC regimen could be a better choice than the MSD HSCT with Bu/Cy regimen for the elderly MDS patients. The encouraging results suggest that the RTC regimen followed by haplo-HSCT is a potentially promising method for older MDS patients. The trail number of the prospective study is "NCT03412409" and the trial URL is "https://clinicaltrials.gov/study/NCT03412409?term=NCT03412409&rank=1".