In recent years, with the development of microelectronics technology, the miniaturization and high integration of electronic devices have put forward higher requirements for thermal flux regulation. Researchers have constructed nanoscale thermal cloaks based on graphene and silicon through molecular dynamics. In our previous study, we found that porous structures have lower thermal conductivity than perfect film. We constructed thermal cloaks by porous silicon structures but did not explore the effect of the hole shape on their cloaking performance. Therefore, in this work, we construct two nanoscale thermal cloaks with square and circular hole structures while ensuring the same void ratio and choosing the perfect film as a reference. The cloaking performance is evaluated by calculating the ratio of thermal cloaking (RTC), and the square hole structure can produce a better cloaking effect. Furthermore, using the phonon localization theory, the underlying mechanism is explained by calculating the phonon density of states (PDOS) and mode participation ratio (MPR). Compared with circular holes, the porous structure of square holes has stronger phonon localization, so the stronger the hindering effect on heat flux, the more obvious the cloaking phenomenon. Our study is beneficial to the development of nanoscale thermal cloaks and can promote the engineering applications of porous structures.