In this paper, ionic liquid treatment was applied to produce nanometric cellulose particles of two polymorphic forms. A complex characterization of nanofillers including wide-angle X-ray scattering, Fourier transform infrared spectroscopy, and particle size determination was performed. The evaluated ionic liquid treatment was effective in terms of nanocrystalline cellulose production, leaving chemical and supermolecular structure of the materials intact. However, nanocrystalline cellulose II was found to be more prone to ionic liquid hydrolysis leading to formation larger amount of small particles. Each nanocrystalline cellulose was subsequently mixed with a solution of chitosan, so that composite films containing 1, 3, and 5% mass/mass of nanometric filler were obtained. Reference samples of chitosan and chitosan with micrometric celluloses were also solvent casted. Thermal, mechanical, and morphological properties of films were tested and correlated with properties of filler used. The results of both, tensile tests and thermogravimetric analysis showed a significant discrepancy between composites filled with nanocrystalline cellulose I and nanocrystalline cellulose II.