Separation of racemic drugs is of great importance and interest in chemistry and pharmacology. Here, we report the bottom-up synthesis of the binaphthyl-based chiral covalent organic frameworks (CCOFs), (R)-BHTP-COF. Then, high-performance liquid chromatography (HPLC) columns were prepared using (R)-BHTP-COF as a chiral stationary phase (CSP). Racemic ibuprofen was successfully baseline-separated on (R)-BHTP-COF-based CSP, and achieved excellent selectivity (α = 2.32) and chromatographic resolution (Rs = 3.39) factors. Meanwhile, the separation of six racemic drugs by the (R)-BHTP-COF-packed column exhibited high resolution, selectivity, and durability. The successful applications indicate the great potential of CCOFs as a novel stationary phase for efficient HPLC separation.