Cellulose nanocrystals were prepared using ionic liquids (ILs), 1-ethyl-3-methylimidazolium chloride [EMIM][Cl] and 1-propyl-3-methylimidazolium chloride [PMIM][Cl], from microcrystalline cellulose. The resultant samples were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The XRD results showed that nanocellulose obtained by treatment with both ILs preserved basic cellulose I structure, but crystallinity index of samples (except for Sigmacell treated with [EMIM][Cl]) was lower in comparison to the starting microcrystalline cellulose. The DLS results indicated noticeably smaller particle sizes of prepared cellulose for material treated with [PMIM][Cl] compared to cellulose samples hydrolyzed with [EMIM][Cl], which were prone to agglomeration. The obtained nanocellulose had a rod-like structure that was confirmed by electron microscopy analyses. Moreover, the results described in this paper indicate that cation type of ILs influences particle size and morphology of cellulose after treatment with ionic liquids.