The invention discloses a disinfectant special for an inspection instrument in the inspection department and a preparation method of the disinfectant. The disinfectant is prepared mainly by the following steps of crushing pawpaw, fructus aurantii immaturus, schisandra chinensis, pericarpium citri reticulatae, smoked plum, chinese holly, pomegranate bark, exocarpium, eucalyptus robusta smith, dogwood, folium eriobotryae, selfheal, myrobalan, corn silk, ligusticum wallichii, glossy privet fruits and pericarpium citri reticulatae viride, soaking, heating and reflowing, wherein an auxiliary material is a filter liquor which is prepared by heating poinsettia, radix angelicae, hemp fimble stem-fibre, subprostrate sophora and fungus-infected rice spike with ethanol and extracting, wherein an additive of polyhexamethylene guanidine is added. The disinfectant is faintly acid, and the environmental acidity can be changed, so that most bacteria which grow best within a PH range of 6.0 to 8.0, have the strongest enzymatic activity and strongly grow and breed cannot exist, and the bacterial growth is effectively inhibited; the disinfectant is easily dissolved in water, and the disinfectant is easily washed out without residues after being used; the disinfectant has the advantages of being small in corrosivity, good in stability and simple in preparation process, can be widely applied to disinfecting the inspection instrument in the inspection department and is suitable for mass production.