An one-transistor-one-bit (1T1b) Flash-based EEPROM cell is provided along with improved key operation schemes including applying a negative word line voltage and a reduced bit line voltage for perform erase operation, which drastically reduces the high voltage stress on each cell for enhancing the Program/Erase cycles while reducing cell size. An array made by the 1T1b Flash-based EEPROM cells can be operated with Half-page or Full-page divided programming and pre-charging period for each program cycle. Utilizing PGM buffer made of Vdd devices in the cell array further save silicon area. Additionally, a two-transistor-two-bit (2T2b) EEPROM cell derived from the 1T1b cell is disclosed with additional cell size reduction but with the operation of program and erase the same as that for the 1T1b cells with benefits of no process change but much enhanced storage density, superior Program/Erase endurance cycle, and capability for operating in high temperature environment.