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The isolator plays a critical role in the scramjet engine situated between the inlet and the combustion chamber. The flow field is more complex with shock–shock interaction and shock boundary layer interaction result in a series of compression waves reffered to as “shock train”. The presence of such flow inside the isolator can degrade the performance of the scramjet engine. The present study focus on the characteristic of the shock train flow field in an isolator and its control by partial removal of the boundary layer. The results examine the variation of the inlet to outlet pressure ratio along with different suction flow ratio. Numerical results indicate that boundary layer suction will cause the slight downstream movement of shock train location and the length of the shock train is reduced. Also when the suction flow gets choked, the transformation of shock train into a single curved normal shock is observed. The effect of varying the upstream boundary layer plays a major role in the suction flow ratio. Furthermore, a significant improvement in the total pressure loss and static pressure rise is obtained by boundary layer suction. The location of the shock train has a greater impact on the performance of the isolator.