A major problem of concern in high-filling engineering is settlement deformations in filling foundation. Such deformations are affected by many factors. In this study, a large-scale centrifugal model test was carried out to study the deformation of high-filling foundation of loess in a gully area, under the conditions of natural water content and rising groundwater respectively. The treatment technology between the original mountain slope and the filling body was also investigated. It was found that the settlement deformations of the high-filling foundation mainly occurred under the condition of increasing centrifugal acceleration. The settlement rate also increased in this process, and the final settlement increased with filling thickness. When the groundwater in the filling body rose, additional settlement in the filling foundation occurred which readily leads to foundation destabilization. Improving the compactness had a significant effect on reducing this additional settlement. Adopting a stepped treatment method to overlap the original mountain slope, the filling body helped to decrease the settlement of the filling foundation above the joint. However, it was not conducive to controlling the settlement of the adjacent filling body. The slope of the original mountain should be taken into account in the design of the overlapping method. For the overlapping region between the filling body and the original rock mass, permeable materials should be installed in the joint which can be compacted to form a permeable zone, which in turn could connect to a drainage pipeline laid at the bottom of the gully. The bedrock fissure water is then efficiently drained and the water infiltrating into the filling body reduced. This could help to avoid a large amount of additional settlement and is beneficial to the foundation's stability after construction.