The thermoelectric properties of a molecular scale junction in the presence of electron-phonon interaction (EPI) that may be used to enhance the thermoelectric performance, are theoretically studied. Such junction is made of trans-PA nanowire connected to similar metallic electrodes. Using the Landauer formalism within the framework of Green's function method and tight-binding (TB) approximation, electronic transport properties including the electronic conductivity (Ge), the thermal conductivity (Ke), the Seebeck coefficient (S), and figure of merit (ZT), are numerically calculated. We used of mapping technique to include the many-body EPI in the calculations. Our results indicate that all thermoelectric characteristics are quite sensitive to EPI and enhance the thermoelectric performance in the trans-PA molecule. Furthermore, it was shown that the figure of merit could be controlled by the coupling strength between the molecule and the electrode.