A cationic cyclodextrin (CD) clicked bilayer chiral stationary phase (CSP) was developed via click chemistry for chiral separations in multimode high-performance chromatography (HPLC). The versatility of this new CSP was evaluated using 17 model racemic pairs including aromatic alcohols, flavonoids and isoxazoline enantiomers in both reversed-phase (RP) and normal-phase (NP) HPLC. The CD functionality-enhanced chiral selectivity was elucidated in different elution modes. Higher chiral resolutions were shown in the RP-elution mode due to the inclusion complexation in comparison to the NP-elution mode. The highest chiral resolution of 4.40 was achieved for 4ClPh-OPr, with 12 racemic pairs baseline separated in RP-HPLC. The addition of organic modifiers in mobile phases plays an important role in optimizing the enantioselectivities of the cationic CD bilayer CSP in NP-HPLC.