Microwave absorbing composites were designed and fabricated by using hybrid carbon based fillers (carbon black (CB) and multi-walled carbon nanotubes (MWCNTs)) as absorbent and phenylethynyl-terminated polyimide as matrix, which have superior mechanical properties and high temperature electromagnetic absorption characteristics. The well dispersion of hybrid fillers enhanced the mechanical properties of the composites due to the particle reinforcement. The complex permittivity increased with the increasing temperature in the X-band frequency from 25 °C to 400 °C. The CB linking the MWCNTs contributed to the absorbing properties. The conductance loss made a major contribution to the loss mechanism at an elevated temperature. When the content of hybrid fillers is 5 wt%, the −10 dB bandwidth is 2.2 GHz and 2.1 GHz with the thickness of 1.7 mm at 25 °C and 200 °C, respectively. Further increasing the temperature would deteriorate the absorbing properties due to the poor impedance matching.