The invention discloses a special disinfectant for examination apparatuses in a clinical laboratory, and a preparation method thereof. The special disinfectant for examination apparatuses in a clinical laboratory comprises, by weight, Greater Celandine Herb, Chinese Incarvilla Herb, Spica Prunellae, root of Cudrania cochinchinensis Kudo et Masam, Wikstroemia indica, Root of Oriental Buckthorn, whiteflower violet herb with root, Cottonrose Hibiscus, dried orange peel, pomegranate rind, dark plum, Immature Bitter Orange, sodium dodecyl sulfate, Cornus officinalis, loquat leaf, sodium sulfosuccinate, pummelo peel, Ligustri Lucidi Fructus, dahurian angelica root, Vietnamese Sophora Root, corn silk, Ligusticum wallichii, fungus-infected rice spike, alkyl alcohol amide, Christmas flower and polyhexamethyleneguanidine hydrochloride. The special disinfectant has the advantages of good stability, high solubility in water, easy flushing and no residual after disinfection, very small corrosion to examination apparatuses, simple preparation process, suitableness for large-scale production, no irritation to human body skins, safety, and no toxic or side effects, can be widely applied to clinical laboratory personnel skin and apparatus disinfection, improves the working efficiency of clinical laboratory personnel, and guarantees the accuracy of an examination result.