Aiming at the difficulty of island power supply and water supply, combining seawater desalination system with micro-grid system, based on the principle of priority utilization of wind power and photovoltaic power generation and participation of battery and diesel engine in dispatching, an optimal economic operation scheme of island micro-grid containing seawater desalination is proposed.To solve the problem that the economic operation optimization algorithm of micro grid is prone to fall into the local optimal and difficult to get the lowest operation cost, an improved niche particle swarm optimization algorithm is proposed, which makes asynchronous change adjustment of learning factor and exponential decline of inertia weight, improving the optimization performance of the algorithm in the optimization process.To consider economic returns of desalination isolated micro power system economic operation cost minimum as the objective, optimization mathematical model is set up, and to improve the niche optimization calculation of particle swarm optimization, and does not consider water desalination system of micro grid economic operation optimization result is compared, the results show that the introduction of the seawater desalination system, improve the economic benefit of the system is also verified the proposed improved niche particle swarm algorithm has good optimization ability.