Ni-based single superalloys play a crucial role in the hottest parts of jet engines. However, due to the complex geometry and macro-segregation during the solidification process, the cast defect such as stray grains is inevitable. Therefore, the transient liquid phase (TLP) bonding which can join several small single crystalline castings together is gradually believed to be an effective method for improving the yields of production of the complex components. The melting point depressant element B is always added into the interlayer filler material. Consequently, borides including the M3B2 and M5B3 phase usually precipitate during the TLP bonding process. So a comprehensive knowledge of the fine structural characteristics of the borides is very critical for an accurate evaluation of the TLP bonding process. In this work, by means of the aberration-corrected transmission electron microscopy, we show, at an atomic scale, the Wyckoff positional order phenomenon of the metal atoms in the unit cell of M3B2- and M5B3-type boride. Meanwhile, the defect along the (001) plane of the above two types of boride are determined to be the polyhedral intergrowth with complex configurations.