A method for fabricating a high-density and high-reliability EEPROM device includes providing a semiconductor substrate having both an EEPROM cell region, and a peripheral MOS transistor region. A gate oxide layer is formed to overlie the peripheral MOS transistor region and the EEPROM cell region. A tunnel oxide region is formed to overlie a portion of the EEPROM cell region. Then, a polycrystalline silicon layer is formed to overlie both the gate oxide layer and the tunnel oxide region. A deuterium annealing process is then carried out to anneal the gate oxide layer and the tunnel oxide region. The polycrystalline silicon layer is patterned to form numerous gate electrodes including gate electrodes for peripheral transistors, floating-gate transistors, and read and write transistors in the EEPROM cell.