Autoantibodies (aAb) against N-methyl-D-aspartate receptor (NMDAR) mediate autoimmune Anti-NMDAR encephalitis. This leads to the development of various symptoms, including seizures, memory deficits, cognitive dysfunction, and psychosis. Our current understanding of the pathophysiology remains limited. Particularly the crucial molecular insights of autoantibody recognition and the influence of their binding on the function of NMDARs. To address these knowledge gaps, we characterized three patient-derived monoclonal antibodies in a multi-modal approach, encompassing super-resolution microscopy, electrophysiology and single-particle cryo-electron microscopy (cryo-EM). Electrophysiological recordings revealed the influence of these three patient-derived aAbs on synaptic NMDAR transmissions, while super-resolution microscopy imaging provided evidence of aAb-specific nanoscale disorganization within synaptic compartments. Furthermore, these aAb-specific mechanisms were supported by structural findings via cryo-EM, which provided further details on various patterns of interactions and diverse epitope recognition. Collectively, these findings provide a novel underlying mechanism involved in anti-NMDAR encephalitis.