The invention discloses a heat pipe composite air conditioning unit for a machine room and a control method of the heat pipe composite air conditioning unit. The heat pipe composite air conditioning unit is characterized in that a heat pipe module and a refrigerating module are combined to form a cold source system in the air conditioning unit, the refrigerating module consists of a compression unit, a condenser, a throttling mechanism, an evaporation channel of an evaporation condenser and the like which form a first working medium circulating loop, the heat pipe module consists of an indoor heat exchanger, a main electromagnetic valve, an air-cooling heat exchanger, a condensation channel of the evaporation condenser, a liquid storage device, a liquid pump and the like which form a second working medium main loop, a bypass branch is arranged between an outlet of the indoor heat exchanger and an inlet of the condensation channel of the evaporation condenser, and a bypass electromagnetic valve is disposed in the bypass branch. A wide annular temperature zone is divided into three functional zones including a refrigerating zone, a composite zone and a heat pipe zone, and working modes of running refrigerating circulation, composite circulation and heat pipe circulation are correspondingly switched and run by the cold source system according to the different functional zones. By the aid of the heat pipe composite air conditioning unit and the control method thereof, utilization of outdoor natural cold sources can be maximized, and low-cost running and energy conservation can be realized.