When it comes to storing energy and releasing it when needed, packed bed storage systems are considered to be one of the most efficient systems available. This paper studies the thermal performance of the melting process in a packed bed system using spherical capsules through CFD modeling. The effective packed bed model was used to simulate the fluid flow in the packed bed and enthalpy porosity method was used to solve the phase change material (PCM) domain. The capsules were filled with three various types of phase change materials, while water was utilized as the heat transfer fluid (HTF). Due to the importance of configurations of materials in the packed beds, the effects of various layouts of them on the performance of the system were investigated. Moreover, Al2O3 nanoparticles as a cheap and easily available nanoparticles were added to the materials. Also, the change in inlet flow rate of the HTF was examined. According to the results, positioning the materials in decreasing order of melting temperature in the flow direction is able to decline the charging time of the system by about 1600 s and increase the charging efficiency by 6.8 %. The addition of Al2O3 nanoparticles was able to decrease the charging time by about 1900 s in the best case and increase the system's efficiency by about 7.5 %. Increasing the inlet flow rate of HTF from 2.5 × 10−5 to 5 × 10−5 (1.5–3 Lit/min) reduced the charging time about 1800 s.