Utilization of biodegradable nanofillers is an emerging approach for the sustainable development of polymer composites. Among numerous green nanofillers, nanocellulose has garnered significant attention because of its abundance, high mechanical strength, and reinforcing capability. However, the intrinsic hydrophilicity of nanocellulose often restricts its homogeneous dispersion in the hydrophobic polymer matrix, resulting in a poor reinforcement effect. In this study, a simple surface modification of cellulose nanofibrils (CNFs) using small hydrophobic molecules is presented. Hydrophobic-modified CNFs have better solubility in organic solvents and exhibit homogeneous dispersion in a thermoplastic polyurethane (TPU) matrix. The molecular interaction between CNFs and the hard/soft segments (HS/SS) of TPU induces surface-mediated crystallization with improved microphase separation of SS and HS. By bridging multiple HS and SS microdomains, hydrophobic-modified CNFs improve the tensile modulus and ultimate tensile strength of the polymer nanocomposites. On the other hand, unmodified CNFs are strongly aggregated in the TPU matrix, which restricts the mechanical reinforcement. These results demonstrate that surface modification of nanocelluloses can engineer their dispersion state and interfacial interaction with matrix polymers, which are crucial for the mechanical reinforcement of polymer nanocomposites.