The invention relates to the field of biological medicine and discloses an application of a targeted adjusting medicine the histone acetylation level in the aspect of preparing a medicine for preventing or treating autoimmune disease. The study finds that after a histone deacetylase inhibitor, namely, valproic acid, is applied to an EAE (Experimental Autoimmune Encephalomyelitis) rat, the disease time of the EAE rat is delayed, the disease symptom is relieved, the morbidity is reduced and the infiltration of CNS (Central Nervous System) inflammatory cells is reduced. The application provided by the invention has the advantage that the histone deacetylase inhibitor, namely, valproic acid, capable of relieving the EAE disease symptom is firstly found. The application provided by the invention has the beneficial effects that: at present, few medicines with small side effects for efficiently treating MS (Metabolic Syndrome) exist; the histone deacetylase inhibitor, namely, valproic acid, is a widely applied medicine for treating epilepsia and is presently used as a clinical trial medicine for treating cancer; and the possibility of using the histone deacetylase inhibitor as the medicine for treating MS disease is huge. The invention provides a new effect target and a medicine source for treating the MS disease.