The coherent structure and instability of the interaction of incident shock wave with boundary layer developing on a compression corner are experimentally studied. The experiments are carried out in a supersonic wind tunnel of Mach number 2. Particular attention is paid to shock patterns and unsteady shock motions induced by the separation bubble. The high-speed schlieren is used to visualize the flowfield evolution and to characterize the instability. The snapshot proper orthogonal decomposition of schlieren sequences is applied to investigate the primary coherent structure in the flowfield. Fast Fourier transform and continuous wavelet transformation are applied to characterize the instability. The results show that there are large-scale low-frequency oscillations of the shock waves and small-scale high-frequency pulsations in the separation region. The peak frequency of shock oscillation is mainly concentrated in the range of 100–1000 Hz. The pulsation of the small flow structure in the separation bubble is mainly concentrated above 12.5 kHz. Based on the results of experimental analysis, the preliminary mechanism of the large-scale instability of such interaction is obtained.