Optimal microstructures for materials getting excellent high-temperature electromagnetic wave absorption (EMA) performance are still not clear since most research has been focused on room-temperature EMA performance. In this paper, amorphous ceramics embedded with isolated SiC nanocrystals or SiC network were obtained by taking advantage of microstructure evolution of polymer derived ceramics (PDCs). Relations between microstructure evolution and temperature-dependent dielectric loss/EMA properties were explored. EMA properties of amorphous PDCs-SiC and sample containing isolated SiC nanocrystals were improved as temperature increased. At 600 °C, reflection loss was smaller than −10 dB over the entire X band for sample thickness in the range of 3.03–3.11 mm, and the minimum value reached −41.8 dB. After formation of SiC nanocrystal network, EMA property of sample decreased with increasing temperatures, which was ascribed, primarily, to rapid increase of conduction loss and consequently deteriorating impedance matching condition. The results indicated that, to obtain excellent EMA property, percolation of EMA agents should be avoided to minimize strong reflection at high temperature. The mechanisms for temperature-dependent dielectric loss and EMA were discussed.