Benefiting from the advantage of weather and illumination independence, less processing data and shorter data time span, spaceborne interferometric synthetic aperture radar technology has certain potential in building 3D reconstruction and urban DSM reconstruction because of its sensitivity to height. However, the phase mixture in the building layover area makes it difficult to realize the accurate building height reconstruction. Therefore, an interferometry model of high-rise buildings was established by comprehensively analyzing the relationship between building structure, scattering mechanisms, and the geometry of interferometric imaging. At the same time, a model-based height estimation method was proposed for high-rise buildings with complex structures and mixed layover interferometric phase. The established interferometry models of buildings are the basis of the height estimation, which reveals the phase mixing mechanism, phase variation characteristics, and the relationship between phase and height. Further, based on the established model, the characteristics and difference of the mixed layover interferometric phase and the pure facade interferometric phase can be obtained. Then, based on these characteristics and by detection of the facade-only imaging area, the pure facade interferometric phase can be recovered from the mixed layover interferometric phase, and the building facade height can be reconstructed by the conversion between phase and height. A pair of TerraSAR-X data located in Harbin city, China was used for experiment and the results show that the height estimation algorithm proposed in this paper can effectively obtain the building height and the DSM in urban area, and for the results of building heights, the average absolute error is within 2 m and the root mean square error is between 2 and 4 m.