Ground-penetrating radar (GPR) has been widely used in estimating the permittivity of mediums. The radar echo amplitude method is an important method used by GPR in this estimation, the basic step of which is to deduce the magnitude of the permittivity according to the relationship between the reflection coefficient and the permittivity. Based on the basic principle of the radar echo amplitude method, this paper proposes a full-wave inversion real-time permittivity estimation method that can be used for stepped-frequency GPR (SFGPR), which offers high efficiency, accuracy, and generalization ability. The characteristics of this method are mainly reflected in the following four aspects: Using the SFGPR system and introducing a layered media detection model, we can complete waveform compensation optimization with high precision. The distance between the antenna and the surface of the reflective medium is extracted from the time domain waveform without manual measurement, avoiding human measurement errors. The inversion of the total reflection waveform at the required height works under the principle of an electromagnetic field, eliminating the need for repeated metal plate calibration experiments and improving work efficiency and waveform accuracy. In a continuous measurement line, the total reflection waveform inversion on each measurement point can be efficiently completed, and the change of permittivity on the measurement line can be obtained. To evaluate the feasibility of the proposed method, we performed experiments on a wall of known thickness, and the permittivity estimation was basically consistent with that of the dielectric probe, physical model calculation, and wall penetration. We also successfully applied this method to the dielectric property analysis of adobe samples. The results indicate that the proposed method can help grasp the condition of a measured medium, which can ensure the accuracy of detection and improve subsequent data processing efficiency.