In the current memory market, many researchers have analyzed the data retention characteristic and predicted the related leakage mechanism. Most studies have shown that the dominant degradation of retention characteristics of Flash memory occurs in the tunneling oxide after program/erase cycling. However, serious degradation of the retention characteristics is also seen in the intrinsic situation before program/erase cycling of devices through the oxide–nitride–oxide (ONO) interpoly dielectric. In this paper, we analyze that degradation by examining the various charge loss mechanisms of the device before cycling and extract two appropriate charge loss mechanisms by comparing the measured $V_\mathrm{th}$ data with the TCAD simulation data, and we verify the mechanisms by extracting the activation energy of each mechanism. We also analyze the effects on those two mechanisms as the ONO thickness and temperature are changed. Based on the results, we establish the intrinsic leakage mechanism through the ONO layers and predict the change in leakage mechanism as the thickness of the ONO layers is decreased.