Clear overlay appliances (COAs) are widely used in orthodontic fields because they offer many advantages, such as cost-effectiveness, good formability, and good optical characteristics. However, it is necessary to frequently replace COAs because the thermoplastic polymers that are used to fabricate COAs have poor abrasion resistance and have a tendency to induce bacterial accumulation. Here, we have developed polysaccharide-based antibacterial multilayer films with enhanced durability, intended for COA applications. First, multilayer films composed of carboxymethylcellulose (CMC) and chitosan (CHI) were fabricated on polyethylene terephthalate glycol-modified (PETG), which was preferred material for COA fabrication, via a layer-by-layer (LbL) technique. Next, chemical cross-linking was introduced within the LbL-assembled multilayer films. The LbL-assembled CMC/CHI film, which was made porous and rough by the cross-linking, formed a superhydrophilic surface to prevent the adhesion of bacteria and exhibited a bacterial reduction ratio of ∼75%. Furthermore, the cross-linking of the multilayer film coated on the PETG also improved the chemical resistance and mechanical stability of the PETG under simulated intraoral conditions with artificial saliva, by increasing the bond strength between the polysaccharide chains. We attempted to accumulate datasets using our experimental design and to develop sophisticated methods to assess nanoscale changes through large-scale measurements.