Moisture migration and distribution in the substructure are found to be the important reasons for water-related problems in high-speed railways. In this study, a numerical model of a double-line ballastless track-bed consisting of a substructure (subgrade surface layer, subgrade bottom layer and subsoil) and a superstructure (including two concrete bases right above the substructure) was established. The superstructure was considered as an impermeable boundary in this model, while two fissures were set at the joint edges of the left-line concrete base and the surface layer, simulating the infiltration area of rainwater. The effects of degree of compaction and fines content of the bottom layer due to moisture migration in the high-speed railway substructure were investigated on this model by applying and analyzing the 2013 rainfall data of Hangzhou, China, for a three-year period. The results show that the saturation zones develop in the subgrade, after a three-year period, with the size increasing with the increase in the degree of compaction or fines content due to higher water retention capacity and lower permeability of the soil. Furthermore, the variations of volumetric water content at different depths of the left-fissure profile indicate that as the degree of compaction or fines content increases, the arriving time of the wetting front increases, but the fluctuation amplitude of the volumetric water content after the arrival of the wetting front decreases on the whole. The degree of compaction appears to present a more significant impact on these two parameters. In particular, a threshold value of the degree of compaction between 0.90 and 0.93 is observed, prolonging the arriving time of the wetting front remarkably at a certain elevation. Besides, it takes a longer time for the wetting front to pass through the interface between the surface layer and the bottom layer for each case. From a practical point of view, it will be beneficial to employ drainage methods to drain out the water before it reaches the bottom layer.