Deep-sea Cone Penetration Test equipment (CPT) and In-Situ Sediment Acoustic Measurement System (ISSAMS) driven by hydraulic penetration system are the important equipment for in-situ detection of seabed sediment. The problems, such as poor position following precision and weak load disturbance rejection performance of the actuator in the hydraulic penetration system are common in the working process of deep-sea CPT and ISSAMS. In this paper, the self-developed deep-sea ISSAMS is taken as the example and various hydraulic penetration system models are established. Most importantly, an optimized control scheme, the fuzzy adaptive PID control scheme with pre-optimization based on genetic algorithm, is presented. To compare with the switch valve controlled hydraulic system used in the ISSAMS physical prototype, the PID control scheme and the fuzzy adaptive PID control scheme are designed as well. It shows that the proportional valve controlled hydraulic system has better position following precision and load disturbance rejection performance than the switch valve controlled hydraulic system and the pump controlled hydraulic system, with more than 95% improvement. The optimized control scheme will further improve the motion-robust performance. Besides, the energy conservation problem is discussed by comparing power requirement and energy consumption of different hydraulic system model and different control scheme. It shows that the pump controlled hydraulic system with the optimized control scheme is the most energy-efficient combination. This paper will have certain reference value to hydraulic penetration system design and motion controller design for deep-sea CPT and ISSAMS equipment.