As a novel non-destructive testing method for roads, ground penetrating radar (GPR) can effectively prevent road water damage by regularly detecting the internal moisture condition of roads. However, when the moisture data of GPR are analyzed, the moisture conditions obtained by relying solely on the analysis of a single profile characteristic may be misjudged. To improve the accuracy and reliability of GPR in detecting the internal moisture content of pavements, focus was placed on the time-frequency domain analysis of GPR moisture content detection profiles in this paper. Simulation tests were conducted, and the influencing factors and results of moisture detection in the pavement surface layer were deeply investigated. Furthermore, the performance patterns of radar detection profiles under different levels of volumetric moisture content of the surface layer were emphatically analyzed. The results indicate that the change in antenna height has a significant impact on the ground reflected wave, while the change in surface layer thickness mainly affects the arrival time and energy intensity of the echo signal at the surface layer-base interface. In addition, as the moisture content of the surface layer increases, the amplitude of the ground reflected wave increases significantly; the arrival time of the reflected wave at the lower interface of the moisture layer is prolonged, and the frequency of the reflected wave within the layer shows a decreasing trend. The research results provide a theoretical basis for detecting the internal moisture content of roads using GPR.