The self-excited shock train oscillation control using partial removal of boundary layer flow in a constant area duct is studied numerically using unsteady Reynolds Averaged Navier–Stokes simulation. The effect of varying the suction flow ratio on the shock train oscillatory characteristics is analyzed using steady and unsteady statistics, space–time contour, power spectra, and cross correlation analysis. For the present study, a constant area duct of height 0.032 mm, and the aspect ratio of 25, at freestream Mach number of 2.0 and back pressure ratio of 0.52 is considered. The removal of the boundary layer through an angled suction slot with three different suction flow ratios is performed. Numerical results indicate that the removal boundary layer restricts the bifurcation process of the shock train and appears to be a single curved normal shock at a higher suction flow ratio. Also, the transition of regular reflection to the Mach reflection type is noted. The suction flow from the top and bottom slot tends to initiate a lateral oscillation that forms a wavy mixing flow region. The power spectral density contour suggests that the increase in suction flow ratio will tend to increase the dominant frequency ranges from (0.034 to 0.094). The cross correlation indicates the presence of downstream pressure disturbance that moves toward the upstream direction. With suction flow, a disturbance that emerges from the suction slot moves in the opposite direction and dominates at a lower suction flow ratio and these disturbances disappear at a large suction flow ratio.