We have proposed a new numerical scheme for the non-Born-Oppenheimer density functional calculation based upon the Green function techniques within the GW approximation for evaluating molecular properties in the full quantum mechanical treatment. We numerically calculate the physical properties of the individual motion in a hydrogen molecule and a muon molecule by means of this method and discuss the isotope effect on the properties in relation to correlation effects. It is concluded that the GW approximation is work well not only for calculation of the electronic state but also for that of nuclear state.