The invention discloses an isolated island operation method and system of an emergency energy storage system of a nuclear power plant. According to the method, after an isolated island starting command is received, the isolated island operation mode is started, and then a storage battery energy storage system is controlled to supply power to nuclear power equipment with power lost. The method for controlling the storage battery energy storage system to supply power to the nuclear power equipment with power lost comprises the steps of controlling the storage battery energy storage system to drive a hydraulic test pump turbonator system and a control system of the storage battery energy storage system to operate normally, controlling the storage battery energy storage system to drive a water supplying assisting system to operate normally, and disconnecting a generator circuit breaker of the energy storage system to start a non-isolated-island operation mode after an external power grid returns to normal and the fact that the grid voltage of a grid-connected circuit breaker is normal and lasts for a preset period of time is detected. According to the isolated island operation method and system of the emergency energy storage system of the nuclear power plant, the nuclear power plant can still operate normally when faced with severe natural disasters, and safety of the nuclear power plant is improved.