Echo separation has long been a challenging and prominent research focus for Multiple-Input Multiple-Output Synthetic Aperture Radar (MIMO SAR) systems. Digital beamforming (DBF) plays a critical role in achieving effective echo separation, but it often comes at the cost of high system complexity. This paper proposes a novel MIMO SAR scheme based on phase-coded waveforms applied to both inter-pulses and intra-pulses. By introducing phase coding in both dimensions and performing joint azimuth–elevation processing, the proposed method effectively suppresses interference arising during the echo separation process, thereby significantly improving separation performance. Additionally, the approach allows for a significantly simplified array configuration, reducing both hardware requirements and computational burden. The effectiveness and practicality of the proposed scheme are validated through numerical simulations and distributed scene experiments, highlighting its strong potential for application in MIMO SAR systems—particularly in cost-sensitive scenarios and systems with limited elevation channels.