Scouring can reduce the strength and rigidity of the pile–soil system and become one of the major causes for the failure of the structure of the partially-embedded single pile. The stratification of the soil fields has a significant influence on the internal force and deformation of laterally-loaded piles. A dynamic model of the laterally-loaded single pile in layered soil is established employing Hamilton’s principle based on the modified Vlasov foundation model. Then, the finite difference method is used to obtain the numerical matrix containing the control equations of the single pile to achieve accurate modeling of the soil–structure interaction (SSI) system affected by scouring, so as to solve the natural frequencies of the single pile. Green’s function method obtains the analytical solution of the forced vibration of the single pile. The effects of scouring and the layered soil on the dynamic response of the single pile are studied by numerical calculation and parameter analysis. It is shown that the dynamic model of the partially-embedded single pile in layered soil based on the modified Vlasov foundation model can accurately predict the dynamic characteristics of pile foundation affected by scouring. As the scouring degree intensifies, the first-order natural frequencies of the single pile in layered soil decrease significantly. The subgrade reaction coefficient of each layer of soil in the modified Vlasov foundation model decreases, and the shear coefficient increases. The first-order natural frequencies of the single pile at each scour level increase with the increase in the thickness of the underlying soil. When the elastic modulus of the first layer of soil is increased by one time, the first-order natural frequencies of the single pile are increased by about 20%.