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Space-time waveform-encoding (STWE)-synthetic aperture radar (SAR) is an effective way to accomplish high-resolution and wide-swath (HRWS) imaging. By designing the specific signal transmit mode, the echoes from several subswaths are received within a single receiving window and overlap each other in STWE-SAR. In order to separate the overlapped echoes, the linear-constrained minimum variance (LCMV) beamformer, a single-null beamformer, is typically used. However, the LCMV beamformer has a very narrow and unstable notch depth, which is not sufficient to accurately separate the overlapped echoes with large signal energy differences between subswaths. The issue of signal energy differences in STWE-SAR is first raised in this paper. Moreover, a novel echo separation scheme based on a second-order cone programming (SOCP) beamformer is proposed. The beam pattern generated by the SOCP beamformer allows flexible adjustment of the notch width and depth, which effectively improves the quality of separation results compared to the LCMV beamformer. The simulation results illustrate that the scheme can greatly enhance the performance of echo separation. Furthermore, the experimental results based on the X-band STWE-SAR airborne system not only demonstrate the scheme’s effectiveness but also indicate that it holds great promise for future STWE-SAR missions.