Calmodulin (CaM) plays a crucial role in metabolism and physiology of eukaryotes by regulating biological activities. Multiple lines of evidences indicate that the phosphorylated flavonoids possess relatively stronger affinities for proteins by forming non-covalent complexes with them, and that the cellular functions are often triggered by this kind of interactions. Chrysin is one of the phosphorylated flavonoids that exist ubiquitously in plants and have remarkably beneficial pharmacological effects. In this study, the molecular docking tools were utilized to investigate the interactions of CaM with chrysin. Two different favorable binding modes have been observed. To complement the results obtained by the molecular docking study, an in-depth investigation into the binding modes was conducted with the molecular dynamics (MD) simulation to explore the binding profile and energy landscape. Based on the results thus obtained, a clear definition of the binding pocket for each of the two binding modes has been revealed. These findings may shed light upon the binding interactions of CaM with chrysin, providing a solid molecular basis for subset analysis of its pharmacological benefits.