This study presents a one-dimensional mathematical model developed to simulate multi-zone thermal storage systems using phase change materials (PCMs). The model enables precise analysis of temperature distribution in the layered storage based on several PCM configurations and properties. It is distinguished by its adaptability to various tank geometries and the number of PCM capsules, enabling its application under diverse operating conditions. By simplifying the implementation of heat transfer processes that depend on the shape of the capsule and the thermal properties of the PCM, the computation time can be reduced to a level that makes simulations over longer periods feasible. Experimental validation confirmed the accuracy of the model, with deviations below 6%, underscoring its practical applicability. The study demonstrates that individual layering in the storage tank can be achieved by filling it with PCMs of different melting points without compromising the maximum storage capacity. It is shown that including a PCM layer can maintain the outlet temperature 20% longer while storing 14% more energy. The results point out the model’s potential to improve the performance of thermal storage systems through targeted PCM layer configurations. The model serves as the basis for the planning and optimization of these systems.