In the present study, the effect of command signals of the flow control valve on performance of underwater discharge systems using a linear pump was investigated numerically. For that, the improved mathematical model was developed. The improvement is to calculate the flow leakage between the water cylinder and the piston. Also the model of the hydraulic cylinder is simplified. To validate the improved model, calculation results were compared with experiment results. The results of the study is as follows: Double ramp command signals of the flow control valve had an advantage over single ramp signals. The parametric study on the effect of double ramp command signals on performance of the system was performed. In case of using double ramp signals, the maximum acceleration of the underwater vehicle was reduced by approximately 50 % compared with using single ramp signals.