Our previous study successfully separated the failure mechanisms that cause charge loss during long-term retention operation of 2-D NAND flash memories using the limiting conditions established by prior literature and experiments. Based on these previous research, we investigated the failure mechanisms during long-term retention (~1000 h) of 3-D NAND flash memories. Each mechanism was separated from the total charge loss measurement data. Program and erase (P/E) cycles deteriorate tunnel oxide quality and increase the contribution rate (CR) of the failure mechanisms associated with tunnel oxide. Our analysis uncovered the dependence that specific parameters related to tunnel oxide have on P /E cycles. It was confirmed that the charge loss function describes the real-world behavior of charge loss mechanisms well. Considering the conditions of how lateral charge loss mechanism occurs by 3-D NAND flash memories’ structural features, the constraints set in previous research was updated, and the validity of these constraints was confirmed by analysis using a TCAD simulation.