Native biopolymer nanofibers (cellulose, chitin, and silk nanofiber) are one of the most important contributors to the outstanding functions and mechanical properties of natural materials. To enhance the mechanical performance, A great deal of top-down routes have been reported to prepare biopolymers nanofibers/nanowhiskers that retaining their nanostructures. Compared with advances in cellulose and chitin nanofibers/nanowhiskers, it remains difficult for direct downsizing the natural silk fibers into silk nanofibers/nanowhiskers (SNFs/SNWs) because of their high crystallinity and sophisticated structures. In this work, environmentally friendly and recyclable deep eutectic solvents (DESs) were used to direct pretreat and downsize natural silks into silk nanowhiskers with high yield. SNWs with similar diameter (3.1-22 nm for OA/ChCl DES treated SNWs, 2.7-20 nm for CA/ChCl DES treated SNWs) and contour length (329 +/- 140 nm for OA/ChCl DES treated SNWs, 365 +/- 200 nm for CA/ChCl DES treated SNWs) to individual nanofibers in natural silk fibers were obtained. In addition, the separated DES with a recovery yield of at least 92% could be reused four times to produce SNWs, indicating the possibility of DESs as green solvents for sustainable biopolymer nanomaterial extraction. Based on the inherent amphoteric properties of SNWs, multicompatibility was explored to facilely composite SNWs with various polymers for preparation of coextruded membranes with enhanced performance and endowed the composites with protein-endowed double adsorption properties. Overall, this work demonstrated that the DES pretreatment process is promising for green and low-cost biopolymer nanomaterial extraction and that the SNWs prepared via DES have good prospects as nanoscale materials in the environmental field and in development of smart biomaterials and drug delivery in biomedicine.