Cytomegalovirus encephalitis (CMVE) is a rare but severe complication following hematopoietic stem cell transplantation (HSCT). However, a comprehensive investigation of its clinical characteristics and potential risk factors remains limited. Our study aims to characterize the clinical features of CMVE patients after HSCT and further explore the risk factors for its incidence. We performed a retrospective nested case-control study on 13 CMVE patients and 52 cases of age- and gender-matched controls by a ratio of 1:4. Clinical data and lab parameters were collected and analyzed. A total of 21 pre- and posttransplantation factors were selected and analyzed by logistic regression for risk factor exploration. Our results show the median age of CMVE patients was 35 years, and the median time from HSCT to diagnosis of CMVE was 134 days. Eight patients (62%) were diagnosed with CMV viremia and five patients (38.5%) presented with EBV infections prior to the diagnosis of CMVE. The most common manifestations were altered consciousness and nausea/vomiting. Imaging findings showed lesions primarily located in the basal ganglia and centrum semiovale. Most of patients had elevated protein and glucose levels in cerebrospinal fluid (CSF). Multivariate logistic regression analysis further showed that posttransplant EBV infection was associated with an increased risk of CMVE. Additionally, patients with medium reconstitution of CD4+CD28+ T cells or high reconstitution were associated with a reduced risk of CMVE compared with poor reconstitution patients. Our findings highlighted the necessity of EBV loads and CD4+CD28+ T cells construction monitoring after HSCT to be alert to the occurrence of CMVE and immediate clinical diagnosis and treatment.