Apart from the trapping of metal ions by the various calixarenes, C-Hexylpyrogallol[4]arenes are studied for their host–guest interactions with the organic guest molecules. In this article, we report the host–guest association of a flavone, baicalein and a chromanone, silybin with C-Hexylpyrogallol[4]arene. The stoichiometry for the inclusion of these guest molecules with C-Hexylpyrogallol[4]arene is determined as 1:1 ratio by Benesi–Hildebrand equation. The strength and mode of binding of baicalein and silybin with is supported by time-resolved fluorescence, nuclear magnetic resonance correlation spectroscopic techniques and molecular docking studies. The structure of the inclusion complex is proposed.