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Airborne three-dimensional SAR uses an antenna array to resolve along height. Then, both the translation and the rotation errors of the plane should be considered. The reasons are that the translation error will result in defocusing along track and the rotation error will lead to phase distortion of signals from different channels. Therefore, the analysis of the motion error of 3-D SAR is much more difficult compared to that of traditional single-channel SAR. In this paper, based on joint multi-channel auto-focusing technology, a motion compensation algorithm is proposed, which can be utilized to estimate not only the translation error but also the rotation error with high accuracy. Hence the motion error would be precisely compensated. Finally, simulation results confirm the validity of the proposed algorithm.