An inorganic-organic hybrid monolithic capillary column was synthesized via thermal free radical copolymerization within the confines of a capillary using a polyhedral oligomeric silsesquioxane (POSS) reagent as the inorganic-organic hybrid cross-linker and a synthesized long carbon chain quaternary ammonium methacrylate of N-(2-(methacryloyloxy)ethyl)-dimethyloctadecylammonium bromide (MDOAB) as the organic monomer. The preparation process was as simple as pure organic polymer-based monolithic columns instead of using POSS as the nanosized inorganic-organic hybrid blocks (cross-linker) of the monolithic matrix. The pore properties and permeability could be tuned by the composition of the polymerization mixture. The characterization and evaluation results indicated that the synthesized MDOA-POSS hybrid monolith possessed the merits of organic polymer-based monoliths and silica-based monoliths with good mechanical and pH (pH 1-11) stabilities, which may be attributed to the incorporation of the rigid nanosized silica core of POSS. Column efficiencies of 223 000 and 50 000 N/m were observed in capillary electro-driven chromatography (CEC) and mu-HPLC, respectively. Peptides and standard proteins were baseline separated by this hybrid column in CEC and mu-HPLC, respectively, as well. The separation of bovine serum albumin (BSA) tryptic digest was also attempted to show its potential application in proteome analysis.