The bulk monomer, butyl methacrylate (BMA), was copolymerized with an ionizable monomer (mono-(2-(methacryloyloxy) ethyl) succinate (MES)) and carbon nanotubes (CNTs) by ethylene dimethacrylate (EDMA) crosslinking to form the porous-layered and nanoparticle-bound stationary phases for open-tubular CEC. Here, two new phases were synthesized to check the role of BMA on the BMA-MES and BMA-CNT phases and the suitability of the MES monomer for concurrently acting as a bulk monomer. One phase, MES-EDMA, was simply composed of MES monomer and EDMA crosslinker and exhibited a phase construction of molecular layers, in contrast to the polymeric phases of BMA-MES. Another phase studied was MES-CNT, which SEM images showed that MES could be a good bulk monomer for a CNT-polyacrylate composite phase with embedded CNTs. For all the modified capillaries, the EOF profiles observed in phosphate buffers between pH 3.6 and 9.6 were comparable with each other and conformed to their corresponding SEM images. The residual silanols retained their influence on the EOF profiles in the MES-EDMA and BMA-MES capillaries, but diminished in the CNT-bound capillaries. In a comparison with the MES-EDMA capillary, the BMA-MES capillary afforded a stronger interaction with flavonoids and phenolic acids and still retained positive capacity factor values. Additionally, the capacity factors obtained from the BMA-CNT capillary were higher than those from the MES-CNT capillary, as the BMA-CNT phase had hydrophobic BMA units and a high surface contact area of bound CNTs.