Background：The anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is the most common autoimmune encephalitis with different clinical presentations. The biomarkers to assess the severity of NMDAR encephalitis are still unclear. Aberrant glycosylation patterns of immunoglobulin G molecules (IgGs) have been found in some neurological and immunological diseases. This study aims to profile the intact N-glycopeptides of serum IgGs and correlate with clinical values in NMDAR encephalitis. Method: A total of 43 patients with NMDAR encephalitis in acute phase and 23 healthy controls (HCs) were included in this study. Patients were classified into 22 mild cases and 21 severe cases according to the mRS score. The human IgGs were purified from serum and digested using trypsin. Tryptic peptides were analyzed directly with our developed N-glycoproteomic method, the combination of electron transfer/higher-energy collisional dissociation and stepped collision energy/higher-energy collisional dissociation mass spectrometry (EThcD-sceHCD-MS/MS). The Byonic software provided subclass-specific and site-specific N-glycosylation qualitative information. The PANDA software provided intact N-glycopeptides quantitative information.