• Developed numerical model of ballasted track-subgrade structure considering precipitation based on FEM/EMLT. • Quantitatively revealed the influence of the subgrade elastic modulus for ballasted track-subgrade structure. • Systematically presented latest materials to improve subgrade waterproofing and drainage performance. Precipitation will cause subgrade elastic modulus ( E s ) to decay as subgrade are composed of fine-grained soil with water sensitivity, resulting in adverse mechanical effects on the ballasted track structure. A numerical model of the ballasted track-subgrade structure was established using the KENTRACK program combining the finite element method (FEM) and elastic multi-layer theory (EMLT), taking into account the non-linearity of the ballast and sub-ballast. The reliability of the developed numerical model was verified macroscopically by a laboratory testing based on vertical compressive stress distribution at the top of subgrade. The mechanical response of the track-subgrade structure and the damage law of the subgrade based on permanent deformation were quantitatively analyzed due to the attenuation of E s . The latest materials for the selection to improve subgrade waterproofing and drainage performance were more systematically presented. The results show that the subgrade surface occurs the stress concentration phenomenon as E s becomes larger, and the subgrade elastic deformation is not sensitive to E s with increasing it to 80 MPa, which the impact mainly appears in the region surrounded by two-axle load and the two rails. In addition, E s decay due to precipitation under constant applied load conditions directly reduces the service life of the subgrade, and the relationship between the allowable number of load repetitions ( N a ) at the top of subgrade and E s can be expressed as a power function. The laying of wicking geotextiles at the top of subgrade, asphalt mixture/PP-modified gravel mixture waterproofing layer, etc. can be utilized to improve the elastic modulus of subgrade due to their excellent waterproofing and drainage performance.