EBV infection is one of the life-threatening clinical complications in patients who underwent haploidentical hematopoietic stem cell transplantation (haploHSCT). Although immune recovery is recognized to be crucial for decreasing subsequent morbidity of infections, the link between T-cell recovery and EBV infection after haploHSCT remains elusive. We recently compared the influences of different doses of antithymocyte globulin conditioning on the T-cell reconstitution post haploHSCT and suggested that CD4-CD8-T cells might interact with the occurrence of EBV reactivation. In the current study, haploHSCT recipients with EBV-DNAemia (n = 64) were compared with a control group without EBV reactivation (n = 192), with regard to the recoveries of T-cell subpopulations. In contrast to other T-cell subpopulations, the median counts of CD4-CD8-T cells in recipients with EBV-DNAemia were significantly lower than the control group at a serial time course (30, 90 and 180 days) after transplantation. Landmark studies further confirmed the correlation of CD4-CD8-T cells with the EBV infection. Multivariate analysis showed that hampered recovery of CD4-CD8-T cells and EBV reactivation were the independent risk factors to predict transplant-related mortality. Our findings may facilitate the intervention strategies to improve the overall survival of haploHSCT recipients.