The hydrogen compression cycle system recycles hydrogen compressed by a compressor at high pressure and stores it in a high-pressure container. Thermal stress is generated due to increase in the pressure and temperature of hydrogen in the hydrogen storage tank during the fast filing process. For the sake of safety, it is of great practical significance to predict and control the temperature change in the tank. The hydrogen charging process in the storage tank of the hydrogen charging station was studied by experimentation and simulation. In this paper, a Computational Fluid Dynamics (CFD) model for non-adiabatic real filling of a 50 MPa hydrogen cylinder was presented. In addition, a shear stress transport (k-omega) model and real gas model were used in order to account for thermo-fluid dynamics during the filling of hydrogen storage tanks (50 MPa, 343 L). Compared to the simulation results with the experimental data carried out under the same conditions, the temperatures calculated from the simulated non-adiabatic condition results were lower (by 5.3%) than those from the theoretical adiabatic condition calculation. The theoretical calculation was based on the experimentally measured pressure value. The calculated simulation mass was 8.23% higher than the theoretical result. The results of this study will be very useful in future hydrogen energy research and hydrogen charging station developments.