This article investigates the effect of embedding the aluminum honeycomb structure in latent heat thermal energy storage (LHTES) of a solar air heater (SAH) and proposes an optimal arrangement of the partial honeycomb core. The effect of placing an aluminum honeycomb core in the LHTES of a solar air heater in mass flow rates of 0.02 and 0.04 kg/s is investigated numerically. A finite volume method is utilized to solve the governing equations in the 3D domain. The phase change material's (PCM's) solid–liquid interface and temperature field are solved by the enthalpy-porosity method and validated by experimental results. The honeycomb core embedded in paraffin is simulated as a composite material with effective thermal properties and local thermal equilibrium condition. The effect of the insertion of eight different honeycomb configurations in the latent heat storage is examined, and an optimized arrangement of the honeycomb structure is proposed. The experimental setup of the SAH is designed based on the optimized honeycomb configuration and is built in the laboratory. The performance of SAH and LHTES is analyzed for three cases: (1) in the presence of a honeycomb (case 8), (2) in the absence of a honeycomb (case 1), and (3) the optimized honeycomb structure (case 2). The results indicate that the honeycomb core in LHTES reduces the melting time by over 35%. Case 2 LHTES (honeycomb in 1/3 bottom portion) is suggested as the best honeycomb structure compared with other configurations. This structure is found to increase the energy storage rate by about 50%, while the energy storage density reduces by 2%. As the thermal performance of the SAH grows after the sunset, the warm air production lasts for a longer duration.