The present invention relates to the technical field of synthetic aperture radar, and in particular to a ground-based interference synthetic aperture radar-based atmospheric phase compensation method. The present invention first uses the inverse fast Fourier transform algorithm to rapidly and effectively realize the focusing in the range and cross-range dimension. Then a triple threshold method which combines coherence coefficient, amplitude, and amplitude dispersion index is used to select reliable PS points. Finally, under a full consideration of the spatial correlation of the atmospheric phase, the atmospheric phase is estimated by using a two-dimensional-polynomial model. The present invention can rapidly and accurately estimate and compensate the atmospheric phase, is helpful in improving the accuracy of GB-InSAR real-time measurement, and valuable and universal in practical application.