Natural polysaccharides have biocompatibility, biodegradability, and nontoxicity, and therefore these can be used as raw materials for biomaterials. Recently, we have developed processes for the fabrication of polysaccharide composite films from polyion complexes composed of chondroitin sulfate C (CS) and chitosan (CHI), denoted as CS/CHI films. The films showed model drug loading and release ability and molecular permeability. On the other hand, the interactions between the molecules and polysaccharides in the films have not been thoroughly evaluated, which should affect the dynamics of these events. In this chapter, the dynamics of molecules in the polysaccharide composite films are described, focusing mainly on two cases. Firstly, the preparation of fluorescein (FL)-loaded polysaccharide composite films (CS/CHI-FL) and evaluation of the ionization and release behavior of FL in CS/CHI-FL were carried out to discuss the dynamics of the loaded molecules in polysaccharide composite films. Furthermore, to clarify the details of different molecular permeation behavior through molecularly imprinted films (IFs), IFs using methylene blue (MB) and a cationic porphyrin derivative (TMPyP) as template molecules (MB-IF, TMPyP-IF) were prepared, and the permeation behavior was investigated when the permeation molecules were changed. These results suggested that the polysaccharide composite films can be applied to pH-responsive materials and drug delivery system (DDS) carriers.