The present work investigated combustion instabilities inside an ethylene-fueled scramjet combustor mounted on a Mach 2.1 direct-connect test facility with an inflow stagnation temperature of 846K. Effects of fueling schemes on the combustion stability characteristics were examined. The experimental results suggest that the oscillation modes correlate with mixing status closely. For the cases with a quasi-steady thermal throat or stable shock trains, flame fluctuation exists in a mode of thermo-acoustic type oscillation with a broad frequency range. For the cases with a transient thermal throat, if a fuel/air premixed region from the injection to the cavity flameholder exists, the cavity pilot flame could reignite the fuel/air mixture and undergo a process similar to deflagration–detonation transition (DDT). This process couples with the flame quenching upstream of the injection location, and a DDT-type low frequency oscillation can be formed.