The objective of this study was to evaluate the effect of O-carboxymethyl chitosan coating on microbiological, physiochemical, and water characteristics of Mongolian cheese during refrigerated storage. O-carboxymethyl chitosan coatings, particularly at 1.5%, improved cheese preservation by significantly inhibiting microbial growth, reducing changes in protein and non-protein nitrogen, and preserving pH and titratable acidity. For texture profile analysis (TPA), the hardness, gumminess, and chewiness in O-CMC treatments were significantly more stable than those in the control during storage. In addition, the relaxation component and image of nuclear magnetic resonance (NMR) were used to analyze the internal water mobility of the cheese during storage. Compared with other treatments, the 1.5% O-carboxymethyl chitosan coating had the best overall preserving effect during storage. O-carboxymethyl chitosan coating could be used in cheese preservation applications and could extend the shelf life of Mongolian cheese. The cheese coated with 1.5% O-carboxymethyl chitosan coating ranked the highest in acceptability at the end of the storage period.