A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$eta$-cyclodextrin ($eta$-CD) complexes, hesperetin/$eta$-CD and naringenin/$eta$-CD. The aqueous solubility of each flavonoid/$eta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$eta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $eta$-CD was responsible for lower aqueous solubility of the hesperetin/$eta$-CD complex.