The invention discloses a multi-source fluid waste heat recovery and comprehensive utilization system which comprises a high-temperature heat exchanger, a heat source end heat exchanger group, a heat source end small-cycle system, a direct heat exchanging device, a heat energy storage device, a use end heat exchanger group, a waste heat utilization system, a heat pump system and an intelligent control system, wherein the intelligent control system is connected with the high-temperature heat exchanger, the heat source end heat exchanger group, the heat source end small-cycle system, the direct heat exchanging device, the heat energy storage device, the use end heat exchanger group and the heat pump system through control cables respectively. According to the system, two independent internal circulations are set, so that dirt and impurities in water can be prevented while the temperature of a heat source end of a heat pump is guaranteed, independent physical and chemical treatment of circulating water can be performed, and the water quality of the heat source end is guaranteed; and besides, mutual contact between the heat pump and liquids containing different components is isolated through internal circulations, the cleaning and maintaining times are reduced, and the stability and the reliability of operating of the heat pump are guaranteed.