Unstable movement of the unstart shock may pose a threat to the safety of a scramjet. The perturbation induced by the unstable movement can also influence the shock structure and the downstream flow, possibly causing a dynamic load on the wall or affecting downstream combustion. Without a thorough analysis of the isolator flow or by ignoring its properties, it is not possible to understand some of the phenomena prevalent in downstream combustion. In this study, two types of instabilities were observed in the unstart shock system. It is shown that if the flow distortion is not severe, the instability in the streamwise direction plays a dominant role. Sequential displacement of the downstream shock was observed in this mode. The time delay between sequential shock motions indicates their response to the movement of the first separation shock. With a highly distorted flow, a flapping mode that resulted in instability in the vertical direction with an asymmetrical effect on the pressures at the walls was observed. In this situation, the shock structure is successively attached to the wall from the head to the tail. By conducting a dynamic mode decomposition analysis, several oscillatory modes, characterized by low-frequency periodicity in the streamwise and vertical directions, were revealed in the shock system. Subsequently, the feasibility of considering the periodical deflection of the incoming flow induced by the significantly unequal amplitudes of shock movements at the two walls as the underlying mechanism for the flapping mode is explored.

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