In this study, a novel mesoporous silica nanoparticles incorporated chiral hybrid monolithic stationary phase was developed. The stationary phase was firstly prepared by an in situ copolymerization of amino-modified mesoporous silica nanoparticles (NH2-MSN), glycidyl methacrylate (GMA), and ethylene dimethacrylate (EDMA) and then functionalized with pepsin as chiral selector. The incorporated mesoporous silica nanoparticles provided additional interactions sites, and in turn yielded different enantioselectivity thus enhancing the overall separation. The column was successfully employed for enantioseparation of fifteen basic chiral drugs in capillary electrochromatography. Effects of nanoparticles percentage, pepsin concentration, the pH of running buffer and the applied voltage were investigated. All the analytes could be eluted in less than ten minutes and nine of them could achieve baseline separation. Satisfactory repeatabilities with relative standard deviations less than 4.2% were achieved through intraday, interday, column-to-column and batch-to-batch investigations. These results indicated that the simultaneous utilization of the unique properties of mesoporous silica nanoparticles and versatile features of monoliths could be a promising strategy for enantioseparation.