China’s southwestern region boasts abundant hydropower resources. However, the area is prone to frequent strong earthquakes. The areas surrounding dam sites typically have deep overburden, and the liquefaction of saturated sand foundations by earthquakes poses significant safety risks to the construction of high dams in the southwest. The effects of liquefaction and reinforcing measures on the foundations of rockfill dams on liquefiable overburden under seismic action are currently the subject of somewhat unsystematic investigations. The paper utilizes the total stress and effective stress methods, based on the equivalent linear model, to perform numerical simulations on the overburden foundations of rockfill dams. The study explores how factors such as dam height, overburden thickness, liquefiable layer depth, liquefiable layer thickness, ground motion intensity, and seismic wave characteristics affect the liquefaction of the overburden foundations. Additionally, it examines how rockfill dams impact the dynamic response, considering the liquefaction effects in the overburden. The results show that although the total stress method, which ignores the cumulative evolution of pore pressure during liquefaction, can reveal the basic response trend of the dam, its results in predicting the acceleration response are significantly biased compared to those of the effective stress method, which comprehensively considers the cumulative changes in liquefaction pore pressure. Specifically, when the effect of soil liquefaction is considered, the predicted acceleration response is reduced compared to that when liquefaction is not considered, with the reduction ranging from 4% to 30%; with increases in the thickness and burial depth of the liquefiable layer, the effective stress method considering liquefaction significantly reduces the predicted peak acceleration; the effect of liquefiable soil on the attenuation of the speed response is more sensitive to the low-frequency portion of the seismic wave. The study’s findings are a significant source of reference for the planning and building of rockfill dams on liquefiable overburden.