This paper presents a design optimisation strategy for a water-based thermal energy storage (TES) unit using phase change materials (PCMs) implemented in the heating, ventilation and air conditioning (HVAC) system of a net-zero energy Solar Decathlon house. This strategy incorporates model-based performance characterisation and a hybrid optimisation technique to maximise the thermal energy storage density of the PCM TES system within a limited night-time charging period. A new mathematical model for the PCM TES with better consideration of heat transfer and thermal energy storage processes was first developed, followed by a sensitivity study to identify the key design variables. The TES unit was then optimised using a hybrid Particle Swarm Optimisation and Hooke–Jeeves (PSOsingle bondHJ) algorithm to maximise its thermal energy storage density for fast charging. It was found that the inner diameter of PCM tubes, the distance-to-diameter ratio of PCM tubes, the type of PCMs, the number of the PCM tubes, and the inlet water temperature significantly affected the charging performance of the TES unit. Compared to an original design without optimisation, the thermal energy storage density of the TES unit using the optimal design identified can be improved from 13.58 to 26.47 kWh/m³. The outcomes of this study could be served as a showcase of how to optimise thermal energy storage in future Solar Decathlon competitions and high performance buildings to facilitate advanced energy management.