A HfAlC composite composed of HfAl4C4 and Hf2Al4C5 was successfully synthesized by the hot-pressing method. The atomic-scale microstructure was investigated through high-resolution transmission electron microscopy (TEM) and Z-contrast scanning transmission electron microscopy (STEM) imaging. The TEM observations revealed that the HfAlC grains had elongated morphologies. There was no amorphous phase in the grain boundary. The microstructure of the composite was characterized by the stacking faults resulted from the insertion of (Al4C3) units, which led to the formation of a new phase Hf4Al12C13 and intergrowth structure between HfAl4C4 and Hf2Al4C5. In addition, the antiphase grain boundary in the ternary-layered ceramics was first observed and the formation mechanism was discussed.