China's hydropower resources are primarily concentrated in the western regions. Due to high-intensity, frequent seismic activity and complex, unfavorable overburden geological conditions, the seismic safety of dams in this area faces severe challenges. Currently, research on the dynamic response of rock-fill dam systems with overburden thickness exceeding 300 meters is relatively scarce. Therefore, this study takes a rock-fill dam constructed on a multi-layered, ultra-thick overburden as a case example. Using the open-source finite element software OpenSees, it systematically investigates the dynamic response of the ultra-thick overburden-rock-fill dam system from three perspectives: seismic motion characteristics, silt layer thickness, and reservoir water level. The research findings indicate: (1) As seismic peak intensity increases, seismic wave attenuation through the overburden becomes more severe, the base acceleration amplification factor decreases, and the dam's amplification effect on seismic waves is weakened. The filtering effect of the soil becomes more pronounced during the propagation of high-frequency-rich seismic motions through the lower overburden. (2) The presence of the clay layer significantly dampens the dynamic response of the upper dam structure, reducing crest settlement by approximately 24.2% and diminishing peak horizontal displacements relative to the dam foundation at various heights along the dam axis. (3) Increasing water storage depth reduces the acceleration amplification factor at the dam crest while having minimal impact on acceleration response at the dam-foundation interface.