The mucus layer acts as a selective diffusion barrier that has an important effect on the efficiency of drug delivery systems in the human body. In this regard, currently the drug nanocarriers of various sizes and compositions are being widely developed to study their mucoadhesive properties i.e., the ability to interact with mucin. However, the effective interaction of drug composition with mucin does not guarantee the success due to the fact that there is a further barrier in the form of epithelial cells retained by calcium ions under the mucus layer. In this work, the interaction of mucin (porcine gastric mucin) with calixarenes is considered for the first time. The study of interaction between calixarenes, mucin and calcium ions by a complex of physicochemical methods showed that effective interaction with mucin requires cationic fragments, and binding with calcium is realized due to anionic fragments in the calixarene structure. Therefore, the combination of different chemical groups in the structure of drug nanocarrier plays an important role in successful mucosal drug delivery. Taking into account the wide possibilities of synthetic modification of the macrocyclic platform, calixarenes can find the application in the drug delivery across mucous barriers.