In this study, core-shell mesoporous silica-carbon composite microspheres (Sil@MC) were prepared by one-step coating of the phenol formaldehyde polymer (PF) on SiO2 surface and by carbonizing the PF polymer under nitrogen atmosphere. The morphology observation of the Sil@MC stationary phase showed that it had good monodispersity. Surface area (302 m2/g), mean pore diameter (9.5 nm), and pore volume (0.63 cm3/g) of Sil@MC materials were also measured by pore structure analysis. The results showed that the Sil@MC was successfully immobilized on the silica particles via copolymerization and carbonization. As a stationary phase of HPLC, the Sil@MC column was filled by a slurry method. The Sil@MC materials formed after calcination of SiO2 coated with phenolic resin could be used for the separation of four polar sugar compounds (D-(+)-glucosamine hydrochloride, glucose, D-(+)-trehalose dihydrat and raffinose) with the mobile phase of acetonitrile-water (containing 0.1% (v/v) formic acid). However, the material formed by calcinating SiO2 without coating phenolic resin could not separate these polar sugar compounds by HPLC-MS. Finally, the representative oligosaccharide isomers of raffinose, melezitose and stachyose, nystose, and human milk oligosaccharide isomers, such as 3'-sialyllactose, 6'-sialyllactose and lacto-N-newtetraose, lacto-N-tetraose, were successfully separated by the Sil@MC column with good peak shapes. The results demonstrates that silica-carbon composites derived from phenolic resin have potential application in polar compounds chromatographic separation.