Given that the performance of the phase change thermal storage device (PCTSD) is limited by the low thermal conductivity of the phase change material, more effective heat transfer structures should be developed to improve the thermal storage rate. In this paper, a novel micro heat pipe array (MHPA)–PCTSD with a highly rational heat transfer structure is proposed to understand the influence mechanism of the relative positions of the MHPA and heat transfer channel. The arrangement of the heat transfer fluid (HTF) channels on both sides of the MHPA (Type A) and the arrangement of the MHPA on both sides of the HTF channel (Type B) are numerically modeled in three dimensions, and the thermal storage performance is analyzed. Results show that Type B has a significant advantage over the traditional heat pipe PCTSD and Type A, which can obtain better temperature uniformity and more reasonable thermal resistance distribution. Moreover, its total thermal resistance and melting time are 17.4% and 21% lower than those of Type A, thus confirming its higher optimization potential.