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Atmospheric disturbance is a main interference for deformation monitoring by GB-InSAR. Most approaches for atmospheric correction are based on the homogenous atmospheric medium assumption that usually does not hold due to complex topography and various environmental factors, leading to low atmospheric correction accuracy. This study proposes two novel model-based approaches for non-homogenous atmospheric compensation in the azimuth and horizontal directions. The conception of a coordinate system is introduced to design the model for the first time. The 2D atmospheric compensation method designed based on the polar coordinate system can address the non-homogenous atmospheric phase screen (APS) correction in the azimuth direction. The 3D atmospheric compensation method based on the rectangular coordinate system deals with the non-homogenous APS in all three directions, and can better address the non-homogenous APS in the elevation direction than the 2D method. Compared with conventional models, the 2D and 3D models consider the other non-homogenous APS conditions in their respective coordinate systems, which helps to broaden the application of model-based approaches. Experiments using different equipment over two study areas are conducted to test the efficiency of the proposed models. The results demonstrate that the proposed approaches can eliminate non-homogenous atmospheric disturbance and enhance the accuracy of GB-InSAR atmospheric compensation, leading to great improvements in slope deformation estimation.