The dynamic response of a low-filled piled embankment under traffic loading is closely related to its bearing capacity and stability. In this study, a series of discrete element numerical models of piled embankments is established by using PFC2D based on the previous indoor model tests. The microscopic parameters of embankment filling and soil between piles adopted in the discrete element model are calibrated by numerical biaxial tests and uniaxial compression tests, respectively. Meanwhile, the validity and feasibility of the discrete element model are verified by comparison of load-transfer efficacy between the discrete element results and experimental data. Then, a cyclic loading in an ideal sinusoidal wave is applied to the surface of a low-filled piled embankment, and the analyses of load-transfer efficacy, distribution of contact force and embankment settlement are performed in detail. Numerical simulation results indicate that the bearing capacity of soil arching in a low-filled embankment would be gradually weakening firstly under the cyclic loading and reach a steady state finally. Specifically, the weakening of soil arching performs as the decreases of the load-transfer efficacy in macroscopic and the difference between the contact forces upon piles and soil between piles in microscopic. Meanwhile, the weakening of soil arching would result in the aggravation of differential settlement on embankment surface.