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Nanocelluloses occur under various crystalline forms that are currently being selectively used for a wide variety of high performance materials. In the present study, two cellulose nanofibers (CF-I) were mercerized by alkaline treatment (CF-II) without degradation, the same molar mass of 560,000 g/mol was measured. Both samples were acid hydrolyzed, leading to cellulose nanocrystals in native (CNC-I) and mercerized (CNC-II) forms. This study focuses on the detailed characterization of these two nanoparticle morphologies (light and neutron scattering, TEM, AFM), surface chemistry (zetametry and surface charge), crystallinity (XRD, 13 C NMR), and average molar mass coupled to chromatographic techniques (SEC–MALLS-RI, A4F-MALLS-RI), revealing variations in the packing of the crystalline domains. The crystal size of CNC-II is reduced by half compared to CNC-I, with molar masses of individual chains of 41,000 g/mol and 22,000 g/mol for CNC-I and CNC-II, respectively, whereas the same surface charge density is measured. This study gives an example of complementary characterization techniques as well as results to help decipher the mechanism involved in mercerization.