Recently, a critical problem of latent heat thermal energy storage remains the low thermal conductivity of phase change materials (PCMs), which can lead to low heat transfer rate. Structural optimization design is an effective solution for this problem. In this work, two horizontal shell-and-tube heat exchangers (HEs) with one inner tube (n = 1) and four inner tubes (n = 4) are designed keeping the same amount of PCM and water flow rate, and their melting and solidification thermal performance and heat transfer characteristics are compared. The results show that in comparison with one-inner-tube HE, the temperature of detected points are affected by both upper and lower inner tubes for four-inner-tube HE, thus the differences in phase change process appear. In addition, the phase change time reduction rates are 34.1%, 33.39%, 28.82% at Tin (inlet water temperature) = 75°C, 80°C, 85°C during charging process, and 17.2%, 27.69%, 36.67% at Tin = 10°C, 15°C, 20°C during discharging process, respectively. In comparison with the one-inner-tube HE, the theoretical efficiency of four-inner-tube HE is increased from 75.88% to 90.34%. Although more friction loss should be paid by four-inner-tube HE, a lower energy consumption and a higher heat-energy ratio are achieved. Based on the results of this study, the amount of cumulative heat per energy consumption is 1.52 × 108 and 2.88 × 108 for one-inner-tube and four-inner-tube HE, respectively.