The invention relates to a comprehensive energy utilization system for desert and an operation method thereof. The comprehensive energy utilization system comprises a wind driven generator, a solar photovoltaic module, a solar heat collector, a heat storage tank, a fermentation tank, a gas storage tank, a biogas generator, a lithium bromide unit, a storage battery energy storage device, a fresh water preparation device, a fresh water reservoir, a psammophyte plantation, a desert animal breeding garden, a water pump and a bitter alkaline water tank. According to the invention, the renewable energy sources of solar energy and wind energy enriched in the desert area are fully utilized, and the generated clean electric energy meets the power consumption of the area. The storage battery energy storage device stores generated surplus electric energy when wind and light resources are rich, the gas storage tank is used for the biogas power generation system, the waste heat utilization system conducts gradient utilization on waste heat of a biogas power generator, and the solar heat collector and the heat storage tank supply energy to the system to achieve multiple guarantees of heat sources.