Natural polymer-derived nanofibrils have gained significant interest in diverse fields. However, production of bio-nanofibrils with the hierarchical structures such as fibrillar structures and crystalline features remains a great challenge. Herein, an all-natural strategy for simple, green, and scalable top-down exfoliation silk nanofibrils (SNFs) in novel renewable deep eutectic solvent (DES) composed by amino acids and D-sorbitol is innovatively developed. The DES-exfoliated SNFs with a controllable fibrillar structures and intact crystalline features, novelty preserving the hierarchical structure of natural silk fibers. Owing to the amphiphilic nature, the DES-exfoliated SNFs show excellent capacity of assisting the exfoliation of several 2D-layered materials, i.e., h-BN, MoS2, and WS2. More importantly, the SNFs-assisted dispersion of BNNSs with a concentration of 59.3% can be employed to construct SNFs/BNNSs nanocomposite membranes with excellent mechanical properties (tensile strength of 416.7MPa, tensile modulus of 3.86GPa and toughness of 1295.4 KJ·m-3) and thermal conductivity (in-plane thermal conductivity coefficient of 3.84 W·m-1·K-1), enabling it to possess superior cooling efficiency compared with the commercial silicone pad.