The invention provides an energy-saving control system of an automatic pressure adjustment waterflooding pump and a waterflooding adjusting method and belongs to the technical field of waterflooding pumps. The energy-saving control system of the automatic pressure adjustment waterflooding pump is characterized in that a high-pressure one-way valve bank (15) and a low-pressure one-way valve bank (19) which are connected with a pressurizing cylinder (1) and a low-pressure work cylinder (10) correspondingly communicate with each other, a throttling distribution device is arranged between the twoone-way control valve banks and comprises a main reversing valve (16), the upper portion of the main reversing valve (16) is connected with a double-action hydraulic cylinder (5), and one side of thelower portion of the main reversing valve (16) is connected with a water trunk line. The energy-saving control system of the automatic pressure adjustment waterflooding pump only adopts one high-pressure cylinder, one low-pressure cylinder and one double-action hydraulic cylinder and does not need to additionally consume capacity, the pressure of the system is monitored in real time and reasonablyredistributed, the energy lost by throttling of a low-pressure well and a high-permeability layer is converted into the energy needed by extra pressurization of a high-pressure well and a low-permeability layer, and the purpose of reasonably utilizing energy is achieved.