During track construction or ballast bed maintenance, ballast layer compaction quality plays an essential role in the following track irregularity accumulation, its lifecycle, and maintenance costs. The ballast compaction process is characterized by its compaction and the accumulation of the stressed state. The elastic wave propagation methods are an effective way for the identification of the ballast bed compaction properties. The paper presents the theoretical and experimental studies of the ballast consolidation under the vibration loading of the sleeper. The practical laboratory study is given by the 1:2.5 scaled physical model of one sleeper and the corresponding ballast layer box. The measurements of ballast pressure and deformations under the vibration loading in the ballast layer and the photogrammetric recording of the ballast flow are carried out. The measurements demonstrate the accumulation of the residual stresses under the ballast layer. Furthermore, the measurements of elastic wave time of flight (ToF) using the shakers under the sleeper and acceleration sensors under the ballast show the substantial increase of the ToF velocities after the tamping process. Moreover, the distribution of the velocities along the sleeper is spatially inhomogeneous. The numeric simulation using the discrete element method (DEM) of the tamping and the testing processes proves the inhomogeneous wave propagation effect. The modeling shows that the main reason for the wave propagation inhomogeneity is the accumulated residual stress distribution and the minor one – the compaction density. Additionally, a method for identifying wave velocity spatial distribution is developed by wave tracing the inhomogeneous medium. The procedures allow ballast identification in the zones outside the shakers.