Solvents that produce cellulose nanocrystals (CNCs) and promote cellulose fibrillation are of current interest. In this work, CNCs were fabricated from cotton at 80 and 100 °C using deep eutectic solvents (DESs) having choline chloride/oxalic acid dihydrate (OA) ratios of 1:1, 1:2 and 1:3. To investigate the side effects of the fabrication, the crystal structure and morphology of micro-sized treated cellulose together with nano-sized CNCs were analyzed by X-ray diffraction, field emission scanning electron microscopy and atomic force microscopy. OA promoted the formation of carboxyl groups on the C6 positions of molecules on the hydrophilic (1–10) lattice planes, causing extensive fibrillation of cellulose and disruption of surface layers on (110) and (200) planes. Lower crystallinity and lamellar structures for CNCs with mild treatment were observed after mechanical disintegration and subsequent lyophilization, which was ascribed to van der Waals forces and hydrogen bonding between adjacent crystalline cellulose chains, accelerating the self-assembly into cellulose macrofibrils. This work is discussed in light of cellulose supramolecular structures that are modified from CNC fabrication via DES treatment, with a view to enhancing the efficacy of treatment by understanding the variations that arise in cellulose structure from a green solvent.