Cellulose nanowhiskers (NWC) have several applications, but its achievement, when held by hydrolysis with strong acids, presents some undesirable aspects as their corrosivity, toxicity and low recovery rate. Recently, [BMIM][HSO4] was proposed as an alternative, but its use has yet disadvantages, mainly due its toxicity and cost. In this sense, this work reports the separation of NWC from MCC by a synthetized protic ionic liquid 2-hydroxyethylamonium hydrogensulphate ([2-HEA][HSO4]) potentially lower toxic than [BMIM][HSO4], which can be easily produced by a low-cost procedure. A stable and polydisperse NWC aqueous suspension was formed exhibiting the birefringence flow typical of nanoparticle dispersions. TEM micrographies confirm needle-shape particles with high average aspect ratio of 50.23 ± 20.93 nm. A good thermal stability was achieved, with Tmax of cellulose decomposition around 234 °C. No ionic liquid residues were observed in the NWC by FTIR analysis. The calculated crystallinity index and crystallite size were 54% and 17.2 nm, respectively. The ionic liquid used in the hydrolysis experiments was successfully recovered in 76.91 ± 0.13% yield, with a similar structure to that of the original ionic liquid. Therefore, [2-HEA][HSO4] was successfully tested as a new, alternative and promising medium to separate cellulose nanowhiskers from cellulosic sources.