Aiming  at  the  problem  of  sustainable  supply  of  energy  resources  in  traditional  islands,  a  multi-time  scale optimal operation method of independent island zero-carbon microgrid is proposed to meet the requirements of stability, flexibility  and  economy  of  independent  island  microgrid.  Firstly,  according  to  the  actual  situation  of  island  energy consumption,  the  wind-solar-storage-hydrogen-water  system  model  of  independent  island  zero-carbon  microgrid  is constructed. Secondly, considering that hydrogen energy storage has the ability of long-term energy storage, a multi-time scale optimization model spanning week-ahead, day-ahead, and intra-day is established, and a multi-time scale operation scheduling strategy considering wind and solar uncertainty is proposed. In the week-ahead stage, the trend of wind and solar resources is predicted based on historical data, and the start-stop plan of hydrogen energy storage is formulated. In the dayahead stage, the stochastic optimization method based on multi-scenario technology is used to deal with the uncertainty of wind and solar energy and formulate the start-stop plan of seawater desalination unit. In the intra-day stage, the operation status of the hybrid energy storage and seawater desalination system is dynamically adjusted in combination with real-time wind and solar data. Finally, the simulation results show that the proposed method can better utilize the characteristics of hydrogen energy storage for a long time to store energy and promote the system’s wind and solar consumption. When the wind  and  solar  resources  are  insufficient,  it  can  effectively  reduce  the  load  loss  and  improve  the  reliability  of  the independent island zero-carbon microgrid system.