The results of the study of the morphology and surface topography of chitosan films of the salt (S-) and basic (B-) chemical form by atomic force microscopy are presented. The films were cast from polymer solutions in acetic, lactic, citric and succinic acid. NaOH and triethanolamine were used for the salt > chitosan base reaction. Surface tomograms were obtained; the main morphological characteristics and roughness parameters of the film samples were estimated. It was found that the morphology, the degree of order, root-mean-square roughness and the height of the surface roughness were determined by the polymer chemical form, the nature of the acid used and the reagent of the polymer-like conversion reaction. The surface of the S-form chitosan films is characterized by fibrillar structural ordering (also dendritic for chitosan succinate), and that of the B-form is globular. The smallest size of surface supramolecular elements was observed for the S-form chitosan films, while the greatest roughness was for the B-form ones. Changing the reagent of the chitosan S > B reaction did not affect the morphological characteristics of the films; however, it affected the microrelief roughness. A more uniform basic chitosan film is formed in an organic base environment. It was suggested that the formation of fibrillar supramolecular structures was due to the unfolding and straightening of macrochains because of the repulsion of the same charged monomer units, while the globular ones were formed due to the folding and densification of macrocoils after neutralizing the total charge of the macrochain.