The use of phase change material (PCM) in thermal energy storage systems can overcome the instability and intermittent problems of solar energy. Heat storage unit (HSU) with capsule structure is introduced in this study to improve the flow characteristics and thermal performance of macroscopically encapsulated PCM HSU. The external flow characteristics and thermal performance of HSU with capsule-shaped and sphere are numerically analyzed. Compared with the traditional sphere HSU, the natural convection in the capsule-shaped HSU is more intense, and the melting time is reduced by 10.1% compared with the sphere HSU. In addition, the flow characteristics of the capsule HSU are more excellent than the sphere HSU, which has lower resistance and resistance coefficient. The optimization results show that with the increase of dimension parameter α, the capsule-shaped HSU has faster melting times and lower resistance coefficient. The capsule-shaped HSU can provide a better external flow characteristic and thermal performance when the dimension parameter α is 2.6.