Exploring the innovative strategies for improving the enantioseparation performance of CDs-based electrokinetic chromatography (CD-EKC) has great significance for chiral separation. In this study, a novel quinine (QUI) modified polydopamine (PDA) coated capillary (QUI/PDA@capillary) was firstly fabricated via the chiral alkaloid-inducing co-deposition strategy and applied for enhancing the enantioseparation performance of CD-EKC using QUI as the immobilized auxiliary modifiers. With the assistance of solvothermal process, the one-pot co-deposition process of QUI/PDA coating was rapidly completed within 60 min, significantly improving the preparation efficiency and simplifying the coating procedure. The successful preparation of the QUI/PDA coated capillary was confirmed by several measurements. Compared with the unmodified, PDA coated and PDA/branched polyethyleneimine (PEI) co-deposited capillaries, significantly improved enantioseparation performances of eight chiral analytes were observed using QUI/PDA@capillary and baseline separation with high efficiency was all easily obtained. The possible mechanism of the remarkably enhanced enantioseparation obtained using QUI/PDA@capillary was also investigated. The relative standard deviations (RSDs) of the enantiomers’ retention times for intra-day, inter-day and column-to-column were all less than 5%. Moreover, the fabricated QUI/PDA coated capillary possessed good stability and long lifetime. These results show the promising prospects of PDA-assisted modification strategy for enhancing the enantioseparation performance and applicability of CD-EKC.