The wave dynamics play a crucial role in the operation characteristics of the rotating detonation engine. We conducted numerical simulations of a rotating detonation combustor (RDC) using multicomponent reactive Navier–Stokes equations coupled with a discrete phases model. The RDC in this research employs a configuration with multiple coaxial injectors supplying oxygen-enriched air and kerosene spray at room temperature. To accurately identify and analyze waves within the RDC, we proposed a three-dimensional transient detonation wave detection method based on the combined parameters of normal Mach number and heat release rate in the flow field. Two typical wave modes, referred to as single-wave mode and counter-waves mode, are identified and then selected to conduct a detailed wave dynamics analysis. The general wave behavior is discussed, and velocity deficit is compared for these two wave modes. For the single-wave mode, intermittent micro-explosions are observed generating retonation waves periodically in the unburnt pockets behind the rotating detonation shock front. For the counter-waves mode, we analyzed the collision process of the two waves and the coupling/decoupling of the shock front with the detonative heat release zone, revealing the reason for significant velocity deficits in this wave mode. This research demonstrates that micro-explosions intermittently occur in the multiphase RDC in both single-wave and counter-waves modes and generate micro explosion shock waves periodically, which influence the complicated wave dynamics behavior.