The baicalein (Ba) is extracted from the roots of traditional Chinese medicine plant, Scutellaria baicalensis Georgi. Ba has attracted more attention for the high medicinal value, but the low oxidation resistance, poor thermal and photostability prevent its application. In this paper, inclusion complexes of Ba and p-sulfonatocalix[n]arenes (SCXn, n=4, 6, 8) were prepared and characterized. The prepared complexes were characterized by fluorescence spectroscopy, Fourier transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy (H-1 NMR), and atomic force microscopy. The fluorescence titration experiment confirmed Ba and SCXn formed inclusion complexes at a stoichiometry of 1:1. A cap-type inclusion mode between the host and guest molecules could infer from H-1 NMR spectroscopy. In addition, antioxidant activity, thermal stability and photostability of Ba were enhanced by forming inclusion complexes with SCXn which were favorable to improving the bioavailability of Ba. Finally, toxicity studies showed that the toxicity of these inclusion compounds Ba/SCXn was not remarkably different from that of the Ba, which was advantageous for the application and development of the Ba/SCXn.