To make appropriate rehabilitation decisions, determining structural layer moduli of the existing semi-rigid asphalt pavements is a crucial task for highway engineers. The objective of this study was to analyze the errors in layer moduli backcalculation due to modeling of layer interface condition. Firstly, according to the full bonding hypothesis, a dynamic finite element analysis model was established to generate a synthetic surface deflection database of the semi-rigid asphalt pavements. Then, the regression functions between deflections basin parameters and layer moduli were created and used to backcalculate layer moduli. Secondly, different friction coefficient values between asphalt layer and stabilized base layer were introduced into dynamic finite element model, accordingly, deflection basin parameters were calculated and layer moduli are determined based on the established regression functions. Finally, the backcalculated layer moduli and the original moduli values were compared. The analysis results demonstrate that assuming full bonding, instead of actual interface conditions of asphalt-stabilized base layer, moduli of stabilized base layers is underestimated, up to 2.5 times smaller than the original values. The improper interface condition of the binder-stabilized base layer has little influence on moduli of asphalt and subgrade layer.