An organic-silica hybrid monolithic capillary column was fabricated by crosslinking (3-aminopropyl)trimethoxysilane (APTMS) modified mesoporous carbon nanoparticles (AP-MCNs) with tetramethoxysilane (TMOS) and n-butyltrimethoxysilane (C4-TriMOS). Scanning electron microscopy (SEM), X-ray photoelectron spectroscopy, mercury intrusion porosimetry and inverse size-exclusion chromatography characterization proved the successful immobilization of mesoporous carbon nanoparticles (MCNs). The crosslinking of AP-MCNs into the hybrid monolithic matrix has significantly increased the reversed-phase retention of alkylbenzenes and chromatographic performance for small molecules separations in comparison with the neat one without MCNs. The resulting column efficiency of the mesoporous carbon nanoparticle-based butyl-silica hybrid monolithic column (MCN-C4-monolith) was up to ca. 116,600 N/m for the capillary liquid chromatography (cLC) separation of butylbenzene. Enhanced performance of proteins separation was achieved on the MCN-C4-monolith in comparison with the butyl-silica hybrid monolithic column without MCN (C4-monolith). The separation of peptides from bovine serum albumin (BSA) digest was carried out on the MCN-C4-monolith by capillary liquid chromatography–tandem mass spectrometry (cLC–MS/MS) with protein sequence coverage of 81.9%, suggesting its potential application in proteomics.