Two types of alginate (Alg) ion complexes were prepared from anionic alginate and two cationic surfactants. The surfactants had the same hexadecyl tail chain and different polar cationic groups: hexadecylpyridinium chloride (HDPyCl) and hexadecyltrimethylammonium bromide (HDTMABr). The Alg ion complexes Alg-HDPy (A-HPy) and Alg-HDTMA (A-HTm) were water-insoluble and soluble in ethanol. The transparent films of the A-HPy and A-HTm were obtained from the alcoholic solutions to study and compare their structures and physical properties using scanning electron microscope (SEM), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), small angle X-ray scattering (SAXS), and tensile test. The results showed that the A-HPy and A-HTm powders and films had distinct structures and physical properties, although they possessed the same alginates and alkyl chains with the same carbon number. This study reports that a variety of cationic moieties have different ion-pair formations and controlled inherent bulk structures and properties. Furthermore, the Alg ion complex films showed antibacterial functions, and there were differences with respect to their biological activities.