An emergency stop system for a hybrid excavator is provided, which includes an emergency switch and an emergency stop unit. In a normal operation state, a power supply that is applied from a power supply unit is provided to a hybrid controller and an engine controller, while when the emergency switch is pressed, the input power supply is intercepted to effectively stop the operation of the hybrid system in the case where equipment abnormality or an emergency situation occurs. Also, when the emergency switch is pressed, the power supply is applied to an emergency alarm unit and an energy discharge unit to notify an operator and neighboring persons of the equipment abnormality and emergency situation occurrence, and a hybrid power source vanishes completely.