Biological phenotype refers to the observable characteristics or combinations of characteristics of an organism, including its morphology or physical form and structure, development process, biochemical and physiological characteristics, behavior and the results of behavior. The concept of phenotype is no longer limited to genetic research, especially after its introduction into autoimmune diseases, that is, not only to find the “origin” of the disease, but also to recognize specific disease entities according to clinical manifestations, to carry out interventions and evaluate the prognosis. In this paper, the scope and significance of clinical core phenotype, intermediate phenotype and endophenotype of neuroimmunological diseases and the approach to understand phenotype of neuroimmunological diseases in depth are discussed.