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Phase unwrapping is a critical step in synthetic aperture radar interferometry (InSAR) data processing chains. In almost all phase unwrapping methods, estimating the phase gradient according to the phase continuity assumption (PGE-PCA) is an essential step. The phase continuity assumption is not always satisfied due to the presence of noise and abrupt terrain changes; therefore, it is difficult to get the correct phase gradient. In this paper, we propose a robust least squares phase unwrapping method that works via a phase gradient estimation network based on the encoder–decoder architecture (PGENet) for InSAR. In this method, from a large number of wrapped phase images with topography features and different levels of noise, the deep convolutional neural network can learn global phase features and the phase gradient between adjacent pixels, so a more accurate and robust phase gradient can be predicted than that obtained by PGE-PCA. To get the phase unwrapping result, we use the traditional least squares solver to minimize the difference between the gradient obtained by PGENet and the gradient of the unwrapped phase. Experiments on simulated and real InSAR data demonstrated that the proposed method outperforms the other five well-established phase unwrapping methods and is robust to noise.