The invention provides a machine room air-conditioning energy-saving operation control system, mainly comprising a control host (1), a temperature compensation box (2) and a temperature sensor (3). The system is characterized in that the temperature compensation box (2) and the temperature sensor (3) are connected with the control host (1) through a data wire to form a complete control system, wherein the control host (1) comprises a temperature set module (11), a temperature detection module (12), a difference comparison module (13), a different determination module (14) and a compensation output module (15); the temperature sensor (3) is arranged on equipment required to be refrigerated; a target object is strictly taken as direction to realize accurate temperature control; the temperature compensation box (2) is made of refrigerating semi-conductor, and is connected with a return air temperature probe on an air return port (41) of an air conditioner (4); and the control host (1) controls the temperature compensation box (2) to perform temperature correction and compensation on return air temperature of the air conditioner (4) at proper time, and controls and adjusts the start and stop operation of a compressor of the air conditioner (4) so as to achieve the designing aim.