A new stationary phase of magnesia–zirconia composite matrix for high-performance liquid chromatography was first prepared by modification of β-cyclodextrin (β-CD) via fosfomycin as a spacer. Various modification procedures were attempted for achievement of successful modification. The modified composite was characterized by using coloration, elemental analysis, diffused reflectance FT-IR, surface area and pore size distribution. The separation of alkylbenzenes, polycyclic aromatic hydrocarbons, positional isomers of some acidic, basic and amphoteric disubstituted benzenes was studied on the new stationary phase. The effect of pH and methanol content in the mobile phase on retention and separation selectivity for the positional isomers were investigated. The chromatographic performance of CD modified magnesia–zirconia was compared with fosfomycin modified magnesia–zirconia as intermediate material and bare magnesia–zirconia as raw material. The results show that various retention mechanisms such as hydrophobicity, inclusion complexation and hydrogen bond interaction exist in the chromatography process of the packing modified with CD. The β-CD played the major role in the chromatographic property of this new stationary phase. The modified magnesia–zirconia exhibits superiority of separation for basic aromatics and high stability above pH 11.