This paper based on a fast implemented multiphase screen method using DFT puts forward an ionospheric Es layer clutter model and uses the newly developed dimensionality reduction space-time adaptive processing- (STAP-) JDL algorithm to suppress Es layer clutter, which proves the validity of the proposed model. Firstly, the multiphase screen method was analyzed, and a fast algorithm using DFT was proposed. Then, based on the multiphase screen method and thorough simulation, we reached a conclusion of the high-frequency radio wave propagation’s fluctuation characteristics in the ionosphere. According to the results of the analysis, a new Es layer ionospheric clutter model was established and was compared with the measured data and verification was made. Finally, based on the built clutter model, JDL algorithm was applied to the high-frequency surface wave radar ionospheric clutter suppression, using the measured data to verify the validity of the model and algorithm. The simulation results showed that the built model can show the characteristics of the ionospheric Es layer clutter and that the JDL algorithm can suppress ionospheric Es layer clutter quite effectively.