The invention relates to an S-(carboxymethyl)-L-cysteine ammonium salt water crystalline pharmaceutical compound (having the following structural formula) and a preparation method and the application of the compound in the preparation of medicines for eliminating phlegm as well as medicines for preventing and treating respiratory system diseases such as chronic obstructive pulmonary diseases (COPD) and the like. After the compound is adopted, the COPD model rat airway resistance is remarkably reduced, the generation of oxide is reduced, the antioxidant level is increased, and the damage of oxide, inflammatory mediator and the like to the lung can be relieved.