This paper demonstrates a novel NAND flash memory structure and annealing configuration including through-silicon via (TSV) inside the silicon substrate to improve annealing efficiency using an electro-thermal annealing (ETA) technique. Compared with the conventional ETA which utilizes WL-to-WL current flow, the proposed annealing method has a higher annealing temperature as well as more uniform heat distribution, because of thermal isolation on the silicon substrate. In addition, it was found that the annealing temperature is related to the electrical and thermal conductivity of the TSV materials. As a result, it is possible to improve the reliability of NAND flash memory. All the results are discussed based on 3-dimensional (3-D) simulations with the aid of the COMSOL simulator.