To calculate and analyze the equivalent resilient modulus of a submerged subgrade, a constitutive model considering the effect of saturation and matrix suction was introduced using ABAQUS's user-defined material (UMAT)subroutine. The pavement response under falling weight deflectometer (FWD) load was simulated at various water levels based on the derived distribution of the resilient modulus within the subgrade. The equivalent resilient modulus of the subgrade was then calculated using the equivalent iteration and weighted average methods. Based on this, the influence of the material and structural parameters of the subgrade was analyzed. The results indicate that the effect of water level rise on the tensile strain at the bottom of the asphalt layer and the compressive strain at the top of the subgrade is obvious, and its trend is similar to an exponential change. The equivalent resilient modulus of the subgrade basically decreases linearly with the rise in the water level, and there is high consistency between the equivalent iteration and weighted average methods. The saturated permeability coefficient and subgrade height have the most significant effect on the resilient modulus of the subgrade, which should be emphasized in the design of submerged subgrades, and the suggested values of the resilient modulus of the subgrade should be proposed according to the relevant construction conditions.