Ground-penetrating radar (GPR) is an important tool for measuring soil water content (SWC) at the field scale. The amplitude analysis of the early time signal (ETS) of GPR may provide a rapid way to estimate SWC. By assuming a homogeneous medium, various studies have been conducted on the relationship between the amplitude of ETS and the topsoil layer’s electromagnetic parameters (dielectric permittivity and conductivity) through numerical simulations, laboratory experiments, and field experiments. Soil is a typical inhomogeneous medium, and soil cultivation is a factor affecting its heterogeneity. In this context, we discuss the ability of the amplitude of ETS to estimate the water content of heterogeneous soil. First, we establish a multi-scale stochastic medium model with the inhomogeneous distribution of dielectric permittivity and conductivity and simulate the GPR response by the finite-difference time-domain (FDTD) method to observe the influence of medium heterogeneity on the GPR response. The heterogeneity of the soil models is evaluated by a geostatistical analysis described by two parameters, correlation length and variability. Then, we analyze the relationship between variability and the average envelope amplitude (AEA) of ETS. A strong soil heterogeneity increases the error of the AEA method in estimating SWC. Finally, the AEA method is used to estimate the SWC of two adjacent fields with different heterogeneities, which were caused by different cultivation methods. The results of the numerical simulation and field experiment indicate that the soil heterogeneity can have an impact on the estimation of SWC using EST, with an error lower than 3% within a depth range of 1/2 λ to λ (wavelength). This suggests that the EST of GPR can be applied to soil layers with relatively large lateral changes in water content.