This paper introduces organic phases with aligned carbonyl groups derived from L-aspartic acid, L-glutamic acid, and L-α-aminoadipic acid; their stationary phases are denoted as Sil-Asp-2C n , Sil-Glu-2C n , and Sil-Adi-2C n , respectively. The stationary phases were used in high-performance liquid chromatography to investigate the alignment effect of carbonyl groups, which act as π-interaction sites, on molecular shape selectivity. The selectivities of the synthesized organic phases were evaluated using polyaromatic hydrocarbons (PAHs), including geometric isomers (e.g., cis-and trans-stilbenes). The PAH selectivities of the prepared stationary phases were higher than that of conventional octadecyl silica. Among the stationary phases prepared in this study, Sil-Glu-2C n (n = 18) showed the highest selectivity toward terphenyl isomers with different twist configurations and the lowest selectivity toward planar PAHs with different aspect ratios. The results show that the molecular shape selectivity of the phases was affected by the alignment of interaction sites. As a practical application of the octadecylated amino acid derivative-bonded stationary phases, we evaluated their selectivity for tocopherol isomers and achieved good separation. Furthermore, Sil-Asp-2C n (n = 1) showed hydrophilic interaction chromatography mode retention behavior for the separation of polar molecules like nucleosides.