In this paper, charge trapping memory (CTM) is studied for analyzing the over-erase phenomenon, based on the first principles and VASP package. The nitrogen vacancy (VN) in Si3N4 and the interstitial oxygen (IO) in HfO2 are selected as model, because of the formation energy. The result about trapping energy shows that the electrons are trapped more easily than holes in these models, so the electrons are selected as programming/erase object. The energy after programming/erase operation, Bader charge analysis, different charge densities, adsorption energy and density of states are all studied to explain the over-erase micro change. The energy and electron change show that HfO2 as trapping layer makes CTM more reliable than Si3N4 as trapping layer; and after a programming/erase cycle, electrons in Si3N4 are erased more than programming ones; and the result of adsorption energy shows that the electrons can exchange more easily in Si3N4 than in HfO2. Finally, the research on the density of states shows that Si3N4 has shallow trapping energy level, HfO2 has deep trapping energy level. In conclusion, the essence of the over-erase in Si3N4 is that the atoms near the defect have weaker localized action on the electrons, resulting in the instinct electrons that are erased in erase operation. The over-erase essence is revealed, which is of benefit to improving the reliability and retention.