A 25,27-bis(l-phenylalaninemethylester-N-carbonylmethoxy)-26,28-dihydroxy- para-tert-butylcalixarene-bonded silica gel stationary phase was synthesized, structurally characterized and used for LC. Its separation mechanism was studied and compared with octadecyl-bonded stationary phase, as well as our previously prepared para-tert-butylcalixarene-1,2-crown-4 stationary phase. Meanwhile, the chromatographic behaviors were investigated by using polycyclic aromatic hydrocarbons, monosubstituted benzenes, anilines, phenols, Tanaka tests solutes, fluoroquinolones, and flavonoids as probes. Mechanisms involved in the chromatographic separation included hydrophobic, π-π and π-electron transfer, hydrogen bonding, and inclusion interactions. Moreover, the column was successfully employed for the analysis of the illegal additive of melamine in milk product.