<p>Natural deep eutectic solvents (NADESs) have attracted considerable attention in the realm of chiral separation. At present, there are few reports on the chiral selectivity differences of NADESs and cyclodextrins with different types in capillary electrophoresis. In this work, a series of choline chloride-based NADESs were coupled with β-cyclodextrin derivatives to construct the binary chiral separation systems. Three binaphthyl atropisomers were selected as the model molecules to investigate the differences in chiral selectivity of the developed separation systems by a self-assembled miniaturized capillary electrophoresis with amperometric detection device (mini-CE-AD) for the first time. An interesting discovery is that the types and stereo-configurations of the hydrogen bond donors in NADESs coupled with the types of cyclodextrins exhibited stereoselectivity differences for the model atropisomers. NADESs based on stereoisomeric organic acids and neutral hydroxypropyl-β-cyclodextrin have played an important synergistic role in improving the resolution of 1,1’-bi(2-naphthol) and 2’-amino-[1,1’-binaphthalen]-2-ol, while choline chloride-urea DES and anionic sulfobutyl-β-cyclodextrin have a better synergistic effect for the separation of 1,1’-binaphthyl-2,2’-diamine. The relative standard deviations of migration time, peak area, and resolution for 1,1’-binaphthol isomers were within 8.6%, and the limits of detection reached 0.060&#xa0;µg·mL^− 1 (S/<i>N</i> = 3). The structure-performance-characteristic relationship of NADESs and cyclodextrins provides new insights for the efficient design and selection of chiral selectors, and the mini-CE-AD system offers a rapid, low-cost, and portable analytical platform for chiral separation. In addition, the greenness and ecological friendliness of this method were evaluated by the modified green analytical procedure index and analytical greenness metric tools.</p> Graphical abstract <p></p>