A cylinder driving system capable of reducing the number of hydraulic devices and the amount of energy loss and an energy regenerating method thereof are provided. To this end, the system includes i) a hydraulic cylinder, ii) a hydraulic pump having three suction/discharge ports of a first port for supplying oil to a bottom chamber of the hydraulic cylinder or draining oil from the bottom chamber, a second port for draining oil from a head chamber of the hydraulic cylinder or supplying oil to the head chamber, and a third port for draining oil from a tank or supplying oil to the tank, the suction rate or the discharge rate in the first port being the sum of the respective discharge rates or suction rates in the second port and the third port, and iii) a driving source for driving the hydraulic pump.