The system of seabed Cone Penetration Test (CPT) is a kind of equipment for offshore investigations. Seabed CPT is used to assess multiple physical properties of marine sediments. Constant-rate penetration mechanism is the core part of seabed CPT, which adopts dual-cylinder drive to penetrate the probe rod into the seafloor sediments at a constant speed (2cm/s). At present, the domestic CPT and its penetration equipment almost all rely on imports. In the process of system design, we found that the traditional PID control of the hydraulic cylinder position control accuracy is low, so we need to study higher precision position tracking control method to achieve uniform penetration of the probe rod. In this paper, a Linear Time-Varying Model Predictive Controller (LTV-MPC) is introduced, which can control two hydraulic cylinders to penetrate probe rod into the seabed sediment with smaller penetration rate error under the condition of changing penetration resistance.