<p>Soft rock fill embankments often experience excessive settlements and even collapse due to the combined effects of traffic loading and rainfall infiltration. In this study, a dynamic loading-seepage device incorporated with a CFD-DEM simulation method was employed to analyze the particle breakage behavior of carbonaceous mudstone fillers and its influence on the permeability coefficient under traffic loading and rainfall infiltration. The results show that under multiple loading sequences, significant loading response is observed at depths of 200–300 mm below the loading surface of the sample, with the maximum relative breakage ratio of particles reaching 0.35. The relative breakage ratio of the carbonaceous mudstone filler gradually stabilizes after 4–6 loading sequences (i.e., 1440–2160 sinusoidal vibrations). The permeability coefficient is mostly affected in the particle breakage development stage, in which the permeability coefficient typically increases to 2–3 times its initial value, and may reach up to 100 times. For carbonaceous mudstone filler with a “skeleton dense” structure, the opening of initial microcracks on particles and the size of inter-particle pores significantly increase under dynamic loading, which is the major reason for the evolution of the permeability coefficient.</p>