The microstructure dependent electromagnetic interference (EMI) shielding properties of nano-layered Ti3AlC2 ceramics were presented in this study by comparing the shielding properties of various Ti3AlC2 ceramics with distinct microstructures. Results indicate that Ti3AlC2 ceramics with dense microstructure and coarse grains are more favourable for superior EMI shielding efficiency. High EMI shielding effectiveness over 40 dB at the whole Ku-band frequency range was achieved in Ti3AlC2 ceramics by microstructure optimization, and the high shielding effectiveness were well maintained up to 600 °C. A further investigation reveals that only the absorption loss displays variations upon modifying microstructure by allowing more extensive multiple reflections in coarse layered grains. Moreover, the absorption loss of Ti3AlC2 was found to be much higher than those of highly conductive TiC ceramics without layered structure. These results demonstrate that nano-layered MAX phase ceramics are promising candidates of high-temperature structural EMI shielding materials and provide insightful suggestions for achieving high EMI shielding efficiency in other ceramic-based shielding materials.