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Nanochitin, especially in the form of chitin nanowhiskers (ChNWs), represents a significant advance in biopolymer technology due to its high specific surface area, superior tensile strength, and excellent thermal stability. Derived from crustacean waste, which contains 15–40% of chitin, these materials provide a sustainable option that diverts waste from landfills and contributes to environmental conservation. Traditional methods of isolating nanochitin are energy-intensive and generate substantial waste. This study introduces a more sustainable method using inexpensive ionic liquids (ILs) such as [Hmim][HSO4] and [HN222][HSO4], which bypass the costly and destructive steps of traditional procedures. This study also identified the byproduct in IL-mediated chitin hydrolysis reaction as calcium sulfate dihydrate and presented a solution to circumvent the byproduct formation. The effectiveness of the [HN222][HSO4] IL in producing ChNWs from both purified chitin and crustacean biomass was assessed, showing a high yield and maintaining the purity and structural integrity of chitin, thereby demonstrating a significant reduction in the environmental footprint of ChNW production.