Based on the incompatibility of water and paraffin and the high thermal conductivity of water, a novel phase change energy storage structure is constructed. The structure is filled with water at the bottom and phase change material at the top. The contact phase transition region is developed using water by numerical method, and the influence of different bottom water volumes on the heat release process of the whole energy storage unit is studied. The results show that the pure PCM unit can ignore the existence of natural convection in the middle and late stages of heat release, and there is a refractory zone at the end of solidification. Increasing the amount of water at the bottom is conducive to the combination of water and paraffin, thus accelerating the solidification of paraffin. This adjustment also causes the cold capacity at the heat source absorption to continue to increase, resulting in a faster drop in the overall water temperature and a more prominent heat transfer effect on paraffin. In Case 3 and Case 5, when the water height is 5.0 mm and 10.0 mm, the solidification time is shortened by 46.57 % and 66.67 %, respectively, compared with Case 1. In addition, the total heat release in Case 3 and Case 5 is reduced by 4.27 % and 9.56 %, respectively, compared with Case 1, indicating that the reduction in total heat energy is relatively small. The further gradient structure design shows that the positive gradient structure is beneficial in increasing the average heat release rate of the unit and reducing the solidification time of the unit.