Cationic and anionic polyelectrolytes, poly(vinylbenzyl trimethylammonium chloride) (PVBTA) and poly(sodium styrene sulfate) (PSSS), were grafted on the surface of the silica particles, respectively, and then these two types of polyelectrolyte-grafted silica particles were applied to the colloidal layer preparation by convective self-assembly (CSA) using hydrophilic or hydrophobic glass substrates to investigate the effect of the interactions between the particles and the substrate surface on the resultant layer structures. When the PVBTA-grafted silica particle (PVBTA-Si) was used, the colloidal monolayers with a non-close-packed (NCP) structure were formed on both hydrophilic and hydrophobic glass substrates, where the NCP colloidal layers on the hydrophobic glass substrate have a somewhat more ordered structure than those on the hydrophilic glass substrate. In the case of the PSSS-grafted silica particle (PSSS-Si), on the other hand, stripe patterns with close-packed (CP) colloidal layers were obtained on both types of the glass substrates. The number of layers of the stripes on the hydrophilic glass substrate was less than that on the hydrophobic glass substrate, while the spacing and width of the stripes on both substrates were similar to each other. The difference in the structures of the colloidal layers obtained here indicates that an attractive interaction, such as an electrostatic attraction and a hydrophobic interaction, between the particle and the substrate surface is necessary to achieve the NCP structure by the CSA process using polyelectrolyte-grafted silica particles.