The energy supply is a key issue for underwater equipment used in seabed exploration, especially in deep water. The high-pressure seawater in deep water contains massive hydrostatic energy and it is a potential clean energy source. The type of energy has advantages of low cost and relatively high reliability in deep water. A novel drive system which converts seawater's hydrostatic energy to mechanical energy is proposed for seabed cone penetration test rig. The hydrostatic drive system uses variable displacement hydraulic motor and PID control method to ensure stabilization of penetration speed and high energy efficiency. The mathematical model of the drive system is built and the comprehensive analysis is conducted. The analysis results based on the real resistance data indicate that the drive system can keep the penetration speed stable when encountering severely fluctuating sediment resistance at different depth of water and achieve high energy efficiency. The mathematical model is validated by the comparison of the results of mathematical model with simulation model based on the commercial software. Because of the high efficiency, the drive system can output considerable amount of energy which is comparable to underwater large battery pack carried by present deep-water cone penetration test rig.