In recent years, multi-input multi-output (MIMO) synthetic aperture radar (SAR) systems, which can promote the performance of 3D imaging, high-resolution wide-swath remote sensing, and multi-baseline interferometry, have received considerable attention. Several papers on MIMO-SAR have been published, but the research of such systems is seriously limited. This is mainly because the superposed echoes of the multiple transmitted orthogonal waveforms cannot be separated perfectly. The imperfect separation will introduce ambiguous energy and degrade SAR images dramatically. In this paper, a novel orthogonal waveform separation scheme based on echo-compression is proposed for airborne MIMO-SAR systems. Specifically, apart from the simultaneous transmissions, the transmitters are required to radiate several times alone in a synthetic aperture to sense their private inner-aperture channels. Since the channel responses at the neighboring azimuth positions are relevant, the energy of the solely radiated orthogonal waveforms in the superposed echoes will be concentrated. To this end, the echoes of the multiple transmitted orthogonal waveforms can be separated by cancelling the peaks. In addition, the cleaned echoes, along with original superposed one, can be used to reconstruct the unambiguous echoes. The proposed scheme is validated by simulations.