Hydrophilic interaction (HI)-based separation like HILIC is effective for analyzing hydrophilic biological samples such as carbohydrates, peptides, and metabolites. To overcome the drawbacks of conventional HILIC such as large consumption of organic solvents and easy deterioration of the separation column, we developed HI electrokinetic chromatography (EKC) by employing bio-based nanomaterials as the hydrophilic pseudo-stationary phase. By mechanical/chemical treatments, cellulose, chitin, and chitosan were processed to 10-nm wide nanofibers/nanowhiskers (NFs/NWs), which are longer/shorter than 1000/200 nm, respectively. In HI-EKC of oligosaccharides using 0.001% uncharged cellulose NFs, strong interaction was observed for the large-size oligosaccharides with the retention factors (k) of up to 1.56, indicating a HILIC-mode interaction. In HI-EKC with 0.1% positively charged chitosan NFs, benzenedisulfonic acid, benzenesulfonic acid (BS), and p-hydroxy BS (HBS) had k values of 0.036, 0.018, and 0.018, respectively, suggesting that the ion-exchange interaction mainly occurred via sulfonate groups. Finally, HI-EKC was demonstrated using 0.05% chitin or chitosan NWs. In both cases using chitin and chitosan NWs, HBS showed much stronger interaction with k > 0.192 compared with BS with k < 0.070. It indicated structural difference between NFs and NWs affected the HI behavior in terms of both the ion-exchange and HILIC modes.