The invention discloses a construction method of a comprehensive energy efficiency evaluation system for a seawater desalination multi-source multi-charge system. The construction method comprises thefollowing steps: analyzing energy efficiency, device energy efficiency, economic energy efficiency, environment and social energy efficiency of the multi-source multi-charge system comprising renewable resources, an energy storage device, refrigeration and heating equipment, a cooling, heating and power load and the seawater desalination device; constructing an energy efficiency index system of the seawater desalination multi-source multi-load system; constructing an energy efficiency index system of the seawater desalination multi-source multi-load system device; constructing an economic energy efficiency index system of the seawater desalination multi-source multi-load system; constructing a seawater desalination multi-source multi-load system environment and social energy efficiency index system; and constructing a comprehensive energy efficiency index system of the seawater desalination multi-source multi-load system by combining the indexes. Therefore, the stable operation of theseawater desalination multi-source multi-load system is ensured, the economic rationality of the system is improved, the renewable resource consumption level, the environmental protection and socialbenefits are improved, and the optimal comprehensive benefits in all aspects are ensured.