In recent years, the high development of high-speed railway lines cross through areas with poor geological conditions, such as soft soil, offshore and low-lying marsh areas, resulting geotechnical problems, such as large settlements and reduction of bearing capacity. As a new soil reinforcement method in high speed railway lines, the piled raft structure has been used to improve soil conditions and control excess settlement. In order to study the dynamic behavior of piled raft supported ballastless track system in soft soil, an experimental study on vibration velocities of piled raft supported embankment and foundations is presented in soft soil with different underground water levels. Vibration velocities at specified positions of the piled raft supported embankment and foundations are obtained and discussed. The vibration velocity curves on various testing locations of piled raft foundations are clearly visible and have sharp impulse and relaxation pattern, corresponding to loading from train wheels, bogies, and passages. Vibration velocity distribution in the horizontal direction at three train speeds clearly follows an exponential curves. Most of the power spectrums of vibration velocity at various locations are mainly concentrated at harmonic frequencies. The change in water level has slight impaction on the peak spectrum of vibration velocity at harmonic frequencies. The vibration power induced by train loads are transmitted, absorbed, and weakened to a certain extent through embankment and piled raft structure. The dynamic response character of embankments are affected by their self-vibration characteristics and the dynamic bearing capacity of the piled raft structure.