We study properties of an interquark potential for the charmed meson systems in lattice QCD. In this study, we propose a new method to determine the interquark potentials together with quark kinetic mass from the equal time QQbar Bethe-Salpteter (BS) amplitude through the effective Schroedinger equation. The study of the interquark potentials at finite quark masses from lattice QCD provides an new way to explore properties of heavy quarkonium states where very rich mass spectrum have been recently exposed in experiments.