When the Lithium-ion battery operates at high temperature, it would bring about short circuit; if it reaches a critical temperature, it will explode. It is important to reduce its maximum temperature by appropriate heat transfer technique. When it operates without an external force for cooling, it needs natural convection technique to take away heat dissipation. Therefore, this study numerically examines three-dimensional transient natural convection of cylindrical lithium-ion batteries inside a rectangular pack with air between cylinders. The heat transfer technique in this study applies PCM (phase change material) between cylinders without or with fin array on top changing distance between cells. The results indicated that for no fin array, the package adopting the PCM could achieve the peak temperature 14.2 °C smaller than the package adopting the air. However, the package adopting the PCM with fin array vertical to the top of the package can best enhance average Nusselt number by 120% compared with using air and no fin array. Replacing the air by the PCM can keep the peak temperature of the batteries within the desirable operation range.