This paper presents the results of numerical simulations examining the thermodynamic processes during hydraulic hydrogen compression, using COMSOL Multiphysics® 6.0. These simulations focus on the application of hydrogen compression systems, particularly in hydrogen refueling stations. The computational models employ the CFD and Heat Transfer modules, along with deforming mesh technology, to simulate gas compression and heat transfer dynamics. The superposition method was applied to simplify the analysis of hydrogen and liquid piston interactions within a stainless-steel chamber, accounting for heat exchange between the hydrogen, the working fluid, and the cylinder walls. The study investigates the effects of varying compression stroke durations and initial hydrogen pressures, providing detailed insights into temperature distributions and energy consumption under different conditions. The results reveal that the upper region of the chamber experiences significant heating, highlighting the need for efficient cooling systems. Additionally, the simulations show that longer compression strokes reduce the power requirement for the liquid pump, offering potential for optimizing system design and reducing equipment costs. This study offers crucial data for enhancing the efficiency of hydraulic hydrogen compression systems, paving the way for improved energy consumption and thermal management in high-pressure applications.