Soil profile stratigraphy plays a fundamental role in the vertical movement of soil water and salt, land cover and land use pattern change in the modern Yellow River Delta. We investigated 22 typical soil profiles with ground penetrating radar (GPR) of 250 MHz antenna according to the tail wing changes over the past 130 years, calculated soil dielectric permittivity and electromagnetic wave propagation velocity with measured soil water content, acquired the electromagnetic wave propagation time from the amplitude-time matrix and finally calculated the thickness of different soil layers. The results showed that GPR can identify the 0-1m soil profile stratigraphy, and soil cultivation layer under different land use patterns is clearly discernible. The comparison of GPR spectrum image and amplitude-time plot is helpful to reduce the estimation error of soil layer thickness. The average error of the estimated soil layer thickness is 0.040m and the error of 54 soil layers in total 58 soil layers is less than 0.100m. The comprehensive effect of soil physical and chemical characteristics affects the electromagnetic wave signals and the profile stratigraphy identification. The more similar the morphological characteristics of spectral images are, the closer the soil properties are. The compound effect of soil water and salt is strong, and the second derivative values of envelop amplitude energy have negative logarithmic function and power function with soil water content and electrical conductivity values, respectively. This study indicated the feasibility of using GPR to investigate coastal saline soil stratigraphy in the modern Yellow River Delta.