The effect of the structure design of a polyelectrolyte cationic and anionic multilayer coating on the liquid– and ink–substrate interaction was studied. The layered structures of anionic–cationic coatings were systematically changed and studied in order to clarify the effect of the polyelectrolyte complexes on the interaction with water-based pigmented inkjet inks. In addition, various amounts of an alkyl succinic anhydride (ASA) were used to increase the hydrophobicity of the base paper before triple deposition of anionic polyelectrolyte (NaCMC) and/or cationic polyelectrolyte (PDADMAC). The coatings were wet-on-wet spray-coated onto the substrates to form various three-layered structures. The results show that the order of deposition of the polyelectrolytes and the ratio between cationic and anionic polyelectrolytes have a significant effect on the print quality. The role of substrate hydrophobicity for the three-layered structure obviously showed that it affected the spreading and wetting behavior of the deposited polyelectrolyte coatings, and subsequently the print quality. The composition of the anionic–cationic polyelectrolyte coatings had a strong influence on the spreading and adhesion of pigmented water-based inkjet inks. The influences of polyelectrolyte structures and composition were more obvious and differentiated when applying on the hydrophilic substrate, revealing the role of ink absorption behavior.