To achieve synergistic reinforcing and cross-linking effect across interface between hydrophilic nanocellulose and hydrophobic rubber, active thiol groups were introduced at reducing end of CNF while retaining hydroxyl groups on the surface, thus forming a percolation network in nanocomposites. The nanocomposites were obtained by casting/evaporating a mixture of dispersed modified CNF and NR in latex form, in which covalent cross-links were formed between thiol groups and double bonds of NR via photochemically initiated thiol-ene reaction. Strong interfacial interaction between NR matrix and end-modified CNF was characterized by Fourier-transform infrared spectroscopy. The structural and mechanical properties of the nanocomposites were evaluated by scanning electron microscopy, dynamic mechanical analysis and tensile tests. Compared to neat NR, the nanocomposite reinforced with 10 wt% modified CNF showed significantly higher values of tensile strength (0.33 to 5.83 MPa), Young's modulus (0.48 to 45.25 MPa) and toughness (2.63 to 22.24 MJ m−3).