Abstract: There are two problems in three-dimensional architecture multi-baseline SAR tomography, the hybrid baseline and the non-uniform baseline. To solve the hybrid baseline problem, this article analyzes and deduces the formula to calculate the impact of hybrid baseline on interferometric phase differences between different scatters for the first time. According to their structures, different compensatory approaches are adopted. For the non-uniform baseline problem, a new method named frequency domain least squares Amplitude and Phase EStimation (APES) is proposed, realizing focusing in the height direction with non-uniform data. The results of simulations and the ALOS data prove the effectiveness of the proposed method.