This research aims to deepen the understanding of the interaction mechanisms between microwave and matter in a metal-ceramic system based on in situ synchrotron radiation computed tomography. A special internal “core-shell” microstructure was discovered for the first time and used as an indicator for the interaction mechanisms between microwave and matter. Firstly, it was proved that the microwave magnetic field acted on metal particles by way of inducing an eddy current in the surface of the metal particles, which led to the formation of a “core-shell” microstructure in the metal particles. On this basis, it was proposed that the ceramic particles could change the microwave field and open a way for the microwave, thereby leading to selective heating in the region around the ceramic particles, which was verified by the fact that all the “core-shell” microstructure was located around ceramic particles. Furthermore, it was indicated that the ceramic particles would gather the microwaves, and might lead to local heating in the metal-ceramic contact region. The focusing of the microwave was proved by the quantitative analysis of the evolution rate of the “core-shell” microstructure in a different region. This study will help to reveal the microwave-matter interaction mechanisms during microwave sintering.