This paper explores a suitable position for a dust-capturing device on the surface of an aeroflyby hypersonic vehicle traveling in the Martian atmosphere at an altitude of 36 km. The feasibility of the Mars aeroflyby sample collection as a mission for capturing Martian dust particles has been investigated by the Japan Aerospace Exploration Agency. In our previous work, trajectories and thermal analyses for spherical dust particles reaching the capturing device were computed. However, Martian dust particles are not all spherical but have several shape variations. In this study, the trajectories and the temperature elevations of disk-shaped particles were numerically investigated. The trajectories were found to deviate and the temperatures were elevated whether the particles faced the disk or the lateral side to the relative flow velocity. For the disk-shaped and spherical particles, the tendencies of the obtained density maps were similar. In contrast, the obtained temperature maps indicated an area divided into high-and low-temperature regions based on differences in the projection area or the stable flight attitude of the disk-shaped particles that cannot be seen in the spherical particles. This study concludes that the leeward and the side surfaces of the aeroflyby vehicle are suitable positions for the dust-capturing device.