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The interferometric synthetic aperture radar (InSAR) technique is widely utilized to measure ground-surface displacement. One of the main limitations of the measurements is the atmospheric phase delay effects. For satellites with shorter wavelengths, the atmospheric delay mainly consists of the tropospheric delay influenced by temperature, pressure, and water vapor. Tropospheric delay can be calculated using numerical weather prediction (NWP) model at the same moment as synthetic aperture radar (SAR) acquisition. Scientific researchers mainly use ensemble forecasting to produce better forecasts and analyze the uncertainties caused by physic parameterizations. In this study, we simulated the relevant meteorological parameters using the ensemble scheme of the stochastic physic perturbation tendency (SPPT) based on the weather research forecasting (WRF) model, which is one of the most broadly used NWP models. We selected an area in Foshan, Guangdong Province, in the southeast of China, and calculated the corresponding atmospheric delay. InSAR images were computed through data from the Sentinel-1A satellite and mitigated by the ensemble mean of the WRF-SPPT results. The WRF-SPPT method improves the mitigating effect more than WRF simulation without ensemble forecasting. The atmospherically corrected InSAR phases were used in the stacking process to estimate the linear deformation rate in the experimental area. The root mean square errors (RMSE) of the deformation rate without correction, with WRF-only correction, and with WRF-SPPT correction were calculated, indicating that ensemble forecasting can significantly reduce the atmospheric delay in stacking. In addition, the ensemble forecasting based on a combination of initial uncertainties and stochastic physic perturbation tendencies showed better correction performance compared with the ensemble forecasting generated by a set of perturbed initial conditions without considering the model’s uncertainties.