Polymorphisms in the granulocyte colony-stimulating factor receptor gene (GCSFR, CSF3R) have been reported to be associated with peripheral blood stem cell enrichment and hematological diseases. The aim of our study was to investigate the effects of donor CSF3R allelic polymorphisms on the outcomes of allogeneic stem cell transplantation. A total of 273 patients who were diagnosed with hematological diseases and treated with allogeneic hematopoietic stem cell transplantation(allo-HSCT) were enrolled in this study. Single-nucleotide polymorphisms in CSF3R were genotyped by targeted next-generation sequencing. There were six types of CSF3R genotypes with percentages over 1%. LFS and OS analyses showed that recipients receiving grafts from healthy donors with an rs3917980 G/G or A/G genotype had higher LFS rates than those receiving grafts from donors carrying an rs22754272 T/C genotype and the double negative group (p=.036) Univariate analysis showed that donor CSF3R with the rs2275472 T/C genotype was associated with higher transplantation-related mortality(TRM) rates (HR=3.77, 95% CI: 1.416-9.631, p=.004) and higher rates of leukemia-free survival(LFS) (HR=2.523; 95% CI: 1.032-6.13, p=.026). In addition, donor CSF3R with the rs3917980G/G or A/G genotype was associated with better overall survival(OS) rates (HR=0.512, 95% CI: 0.244-1.017, p=.047). Our findings demonstrate the important prognostic value of genetic variations in donor CSF3R to predict clinical outcomes in patients undergoing allo-HSCT.