Background Neuromyelitis optica (NMO), multiple sclerosis (MS) and autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy belong to autoimmune diseases incentral nervous system mainly manifestate encephalomyelitis. The glycocalyx (GLX), consists of several membrane-bound macromolecules, is located on the luminal side of the endothelium and mediates the blood and the vessel interaction. Until now, there is still lacking a holistic understanding of the GLX degradation in autoimmune encephalomyelitis. Aim This study aimed to detect the shedding levels of GLX components, heparan sulfate (HS) and hyaluronic acid (HA) in serum and cerebrospinal fluid (CSF), correlate them with the severity and assess the diagnostic value of them, and evaluate their correlations with pro-inflammatory cytokines. Methods Serum and CSF samples were obtained from 24 NMO patients, 15 MS patients, 10 autoimmune GFAP astrocytopathy patients, and 18 controls without non-inflammatory neurological diseases. Soluble HS, HA and IFN-γ, IL-17A, matrix metalloproteinase (MMP)-1 were detected by enzyme linked immunosorbent assay ELISA. Results Besides levels of serum and CSF levels of HS, HA and related cytokines were significantly elevated in these diseases. Notably, HS, HA in NMO, MS patients, and autoimmune GFAP astrocytopathy diseases were widely correlated with EDSS scores. Importantly, the ROC curve analysis suggested a potential diagnostic role of HS or HA . Conclusions The results here suggested the GLX degradation and inflammation in NMO, MS and autoimmune GFAP astrocytopathy. Moreover, increased shedding of HS or HA may indicate worse clinical situation. Importantly, CSF HS and HA may be informative diagnostic biomarkers for telling autoimmune encephalomyelitis from the non-inflammatory neurological controls. Furthermore, therapeutic strategy for protecting GLX may be effective to these diseases.