Purpose: Achieving high-quality immune reconstitution (IR) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is directly associated with the patient’s ability to resist infections, prevent tumor relapses, and suppress graft-versus-host disease (GVHD). The status of CD4 + T cells is critical for reconstituting adaptive immunity after transplantation; however, the patterns of reconstitution and their influencing factors remain unclear. Methods: This retrospective cohort study involved 164 patients who underwent myeloablative allo-HSCT from April 2016 to May 2023. Based on the early post-transplantation CD4 + T cell counts, the cohort was divided into two groups: 73 patients with high-quality IR (HIR) and 34 patients with low-quality IR (LIR). LIR was associated with an increased risk of Epstein–Barr virus (EBV) reactivation following transplantation. Plasma EBV viral load was monitored weekly using quantitative PCR for the first 100 days post-transplantation. Results: The LIR group had a higher viral load at the time of the first EBV reactivation and a significantly earlier first reactivation compared to the HIR group. No significant differences were observed in overall survival, GVHD incidence, or relapse rates between the groups. A CD4 + T cell count of < 60 cells/μL within 30 days post-transplantation was associated with a higher incidence of EBV viremia compared to the control group. Conclusion These findings suggest that early CD4 + T cell counts may serve as a predictive marker for post-transplant EBV infection.