The valve-controlled hydraulic cylinder system (VCHCS) is commonly utilized in the underwater manipulator, which is the most important tool for subsea tasks. Hydraulic oil viscosity is very sensitive to pressure. Therefore, when working at different depths under different ambient pressures in the sea, the hydraulic oil viscosity and the pipeline pressure loss in the deep-sea VCHCS vary greatly, which seriously affects the energy efficiency of the system. In addition, the control accuracy of the deep-sea VCHCS is also influenced by changes in the hydraulic oil viscosity and the pipeline pressure loss. In order to realize energy-saving control, this research introduces a proportional relief valve and develops a variable pump pressure control strategy. At the same time, a variable gain proportional-integral-derivative (PID) algorithm is designed to achieve precise control. A co-simulation model of the deep-sea VCHCS is then established, and many simulation analyses are carried out. Compared with traditional PID control with a constant pump pressure, the proposed method presents advantages such as lower energy consumption, better control accuracy, better resistance to load impact, and accuracy consistency under different working depths. Among them, when working at 11 km depth in the sea, the proposed method is capable of saving energy by 36.5% for the multi-step movement, by 30% for the harmonic movement, and by 47% for the complex movement. The present work in this research provides a solution that can realize energy saving and precise control of the deep-sea VCHCS at the same time in the wide span of depth in the sea.