The utility model discloses a low power usage effectiveness (PUE) high-density liquid-cooling energy-saving machine room cooling system, which comprises a machine room, a machine cabinet, an air conditioner box, a compressing, cooling and circulating system formed by a compressor, a condenser, an expansion valve and an evaporator, and a natural cooling and circulating system formed by a natural cooler and a water coiler of the air conditioner box. An outlet of the water coiler of the air conditioner is communicated with an inlet of an electric three-way valve, and two outlets of the electric three-way valve are respectively communicated with an inlet of the water coiler and an inlet of a water coiler of the natural cooler. A micro-computer control system is respectively and electrically connected with the compressing, cooling and recycling system, the natural cooling and circulating system, the electric three-way valve, a first temperature sensor arranged outside the natural cooler, a second temperature sensor arranged on a back door portion of the machine cabinet and a third temperature sensor arranged on a water inlet tube portion of the water coiler of the air conditioner box. The low PUE high-density liquid-cooling energy-saving machine room cooling system can automatically adjust the output capability of the compressor, fully utilizes external cooling sources and achieves accurate energy saving.