In this article, the bonding characteristics of perfluoropolyether (PFPE) molecules, having a hydroxyl end group, regarding Si-incorporated amorphous carbon surfaces were investigated. The Si contents in the carbon films were varied from 0 to 10.3 at. %. The PFPE lubricant layers were deposited on the carbon surfaces using the traditional dip coating and vacuum vapor deposition. It was found that the Si incorporation enhances the bonding of the PFPE molecules on the carbon surfaces. Moreover, the bonding of the PFPE molecules increases with the increasing Si content in the carbon film. This is attributed to the structural and chemical modifications of the hydrogen-terminated carbon surfaces due to the Si incorporation into the carbon network, which increases the adsorption sites for the PFPE molecules. The bonding of the PFPE molecules is enhanced using a vapor deposition technique compared to the traditional dip coating. The Si-incorporated carbon films represent a reasonably high hardness and a good bonding characteristic for the PFPE molecules, which could be good candidates as a protective coating for magnetic storage disks.