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Haploidentical hematopoietic stem cell transplant (haplo-HSCT) is an upfront and effective therapy for hematology patients, but it usually has many complications, such as neurological complications. As one of the neurological complications following haplo-HSCT, immune-mediated demyelinating diseases of the central nervous system (CNS) seriously affect a patient's quality of life. However, the incidence, risk factors, and pathogenesis of CNS demyelination are not very well understood. Thirty of the 1526 patients (1.96%) suffered from CNS demyelination. In univariate analysis, we found that blood-brain barrier (BBB) permeability and the CSF IgG synthesis index (IgG-Syn) were related to the occurrence of CNS demyelination (p < 0.05). In a multivariate analysis, the IgG-Syn (OR = 1.017, 95% CI 1.003-1.031, p = 0.019) and CSF anti-myelin oligodendrocyte glycoprotein antibody (MOG.Ab) (OR = 12.059, 95% CI 1.141-127.458, p = 0.038) were independently associated with the onset of CNS demyelination. We also studied the possible pathogenesis of CNS demyelination. Immune reconstitution (the cell proportions of CD19 + B cells, CD3 + T cells, and CD4 + T cells); the counts of leucocytes, lymphocytes, monocytes, and platelets; and the levels of immunoglobulins A, G, and M 30, 60, and 90 days after HSCT showed no significant differences between CNS demyelination and no demyelination (p > 0.05). The probabilities of overall survival showed no significant differences between patients with and without demyelination (p > 0.05). Only four deaths in 30 patients, but bringing projected survival to less than 20%.We imply that IgG-Syn and CSF MOG. Ab may be associated with the onset of CNS demyelination during 2 weeks of neurological symptoms in patients with brain or spinal cord MRI abnormality. Immune reconstitution may not be the pathogenesis of CNS demyelination.