The invention relates to an energy-saving machine room air conditioning system and a running method thereof. The energy-saving machine room air conditioning system comprises a first circulation loop for refrigerating; the first circulation loop comprises a pump, a liquid storage tank, a condenser, a compressor, an evaporator and an expansion valve which are sequentially connected in series, a first one-way valve is connected to the two ends of the pump in parallel, and a second one-way valve is connected to the two ends of the compressor in parallel; the energy-saving machine room air conditioning system further comprises a second circulation loop used for pre-lowering the inflow air temperature of the condenser, and the second circulation loop lowers the inflow air temperature of the condenser through a natural cold source. According to the system, the circulation system capable of achieving precooling through the natural cold source is additionally arranged, therefore, the inflow air temperature of the condenser in the energy-saving machine room air conditioning system is lowered, the annual working time of the pump in the first circulation system for refrigerating in an air conditioner is prolonged, the time for achieving refrigerating through cold energy of the outdoor natural cold source is prolonged, and then the annual energy efficiency ratio of the energy-saving machine room air conditioning system is increased.