In this article, we demonstrate the first surface modification of cellulose nanocrystals (CNCs) with quaternary ammonium-containing ionomers by ionic binding of their positively charged ammonium ions onto the negatively charged surface of CNCs. A range of hyperbranched polyethylene ionomers (I1–I6) having different ionic content (0.2–2.3 mol %) has been designed and employed for this purpose. The simple dropwise addition and mixing of the aqueous dispersion of CNCs with the ionomer solution in tetrahydrofuran (THF) conveniently renders the ionomer-modified CNCs (mCNC1–mCNC6). The presence of adsorbed ionomers on the modified CNCs is confirmed with spectroscopic and X-ray diffraction evidence and quantified through thermogravimetric analysis. The effects of the ionomer to CNC feed mass ratio and the ionomers of different ionic content on the modification have been examined. A study on the morphology of the modified CNCs by atomic force microscopy discloses the occurrence of side-to-side and/or end-to-end assembly of the CNC rods due to the “cross-linking” or bridging effects of the multidentate ionomers. Because of the hydrophobic hyperbranched polyethylene segments in the adsorbed ionomers, the modified CNCs can be dispersed in nonpolar or low-polarity organic solvents (such as THF, toluene, and chloroform). In particular, the THF dispersions of modified CNCs prepared with ionomers having ionic content ≥0.7 mol % (I3–I6) behave as thixotropic organo-gels at concentrations ≥40 mg mL–1. Further, the modified CNCs better disperse than unmodified CNCs in a hydrophobic ethylene–olefin copolymer (EOC) elastomer matrix and show better thermal stability than a surfactant-modified CNC sample. Tensile testing confirms that the EOC composites, filled with the ionomer-modified CNCs, are significantly reinforced with a tensile modulus nearly doubled that of neat EOC, and they demonstrate better elongation at break relative to those filled with unmodified CNCs or surfactant-modified CNCs.