Regioselectively substituted nanocellulose was synthesized by protecting the primary hydroxyl group. Herein, we took advantage of the different reactivities of primary and secondary hydroxyl groups to graft large capping structures. This study mainly focuses on regioselective installation of trityl protecting groups on nanocellulose chains. The elemental analysis and nuclear magnetic resonance spectroscopy of regioselectively substituted nanofibrillated cellulose (NFC) suggested that the trityl group was successfully grafted in the primary hydroxyl group with a degree of substitution of nearly 1. Hansen solubility parameters were employed, and the binary system composed of an ionic liquid and pyridine as a base was revealed to be the optimum condition for regioselective functionalization of nanocellulose. Interestingly, the dissolution of NFC in the ionic liquid and the subsequent deprotection process of NFC substrates hardly affected the crystalline structure of NFC (3.6% decrease in crystallinity). This method may provide endless possibilities for the design of advanced engineered nanomaterials with multiple functionalities. We envisage that this protection/deprotection approach may lead to a bright future for the fabrication of multifunctional devices based on nanocellulose.