Determining the deformation trend of silt subsoil under long-term aircraft loading by conventional numerical methods based on finite elements is challenging and poses several limitations. In this study, a boundary surface model for remolded saturated silt considering the influence of the soil dry density was developed, and an explicit integral algorithm with error control was used to incorporate the model into a user-defined material subroutine that the finite element software (ABAQUS 6.14) could call. In this way, the consolidated undrained dynamic triaxial test of a soil unit was established for simulation and model validation, which corroborated that the model could describe the dynamic properties of the saturated silt. Then, a numerical model of the runway with layered compaction and different compaction degrees was also developed to numerically analyze the deformation of the subsoil under cyclic aircraft loading. The results showed that the subsoil deformation increased continuously with the increase of cycle number. However, the deformation rate decreased gradually, and the silt subsoil deformation remained stable after 50 loading cycles. After the same number of loading cycles, the cumulative plastic deformation of the subsoil model with the overall compaction degree of 94% was smaller than that of the model with layered compaction. It was also shown that different aircraft speeds have minimal effect on the cumulative plastic deformation of the subsoil. Nevertheless, the ultimate cumulative plastic deformation is larger, as the loading duration is longer at low aircraft speeds. It indicates that strictly controlling of the compaction degree within a certain range of load influence is imperative in practical engineering, as it reduces the associated costs.