In order to reveal the unsteady flow characteristics during the pre-compression process of the radial wave rotor combustor, the pre-compression mechanism induced by complex wave systems under typical operating conditions was simulated and analyzed using three-dimensional unsteady simulations. The impact of pressure differential across intake and exhaust ports, as well as rotor speed, on the propagation behavior of compression waves within the channels was focused on. The results indicate that as compression waves propagate within the channels, they are influenced by the curvature of the curved channels, leading to wave reflection, refraction, and attenuation. This results in energy loss and waveform distortion, which affect the propagation path and speed of the compression waves. Although a higher pressure difference enhances the intensity of the compression waves, it exacerbates overfilling of the fuel and flow instability, increases thermodynamic losses, and significantly reduces the isentropic compression efficiency. The rotational speed affects the propagation characteristics of compression waves within the channels by adjusting the operational timing of the wave rotor. At 1 200 r/min, the opening time of the intake port is extended, causing the compression waves to reflect and form expansion waves that propagate in the reverse direction. This results in a pressure ratio within the channel of only 103% and a substantial decrease in isentropic compression efficiency.