The influence of the conditions of the formation of genipin cross-linked chitosan cryostructurates on the porous morphology and physicochemical properties of these cryostructurates and on the possibility of their use as biopolymer 3D scaffolds for tissue engineering was studied. The chitosan cryostructurates were obtained by freeze-drying a chitosan acetate solution, treating the resulting sponge with an alcohol solution of ammonia to transform the polyaminosaccharide from a salt into a chitosan-base, and then cross-linking the polymer with genipin (the molar ratios of genipin to the number of chitosan amino groups were 0.05, 0.033, and 0.02, respectively). The pore sizes, water-holding capacity, and in vitro biodegradation rate of the cryostructurates were shown to depend on the aforementioned ratio. The properties of the prepared chitosan cryostructurates, the hydrogels formed by chitosan cross-linking with genipin at positive temperatures, and the films cast from genipin-containing chitosan solutions after solvent evaporation were studied and compared. The biocompatibility of the obtained macroporous sponge materials was demonstrated using L929 mouse fibroblasts. Confocal laser microscopy showed that the cells in all of the 3D scaffolds obtained were evenly distributed; they grew and proliferated when cultured in vitro for seven days.