The present invention discloses a low voltage difference-operated EEPROM and an operating method thereof, wherein at least one transistor structure is formed in a semiconductor substrate and each includes a first electric-conduction gate. Same type ions are implanted into a region of the semiconductor substrate, which is near interfaces of a source, a drain and the first electric-conduction gate, or ion-doped regions of the source and the drain, to increase the ion concentration thereof, whereby to reduce the voltage differences required for writing and erasing. The present invention also discloses an operating method for the low voltage difference-operated EEPROM, in addition to the EEPROM with a single gate transistor structure, the present invention also applies to the EEPROM with a single floating gate transistor structure.