In the Northwest Loess Plateau of China that is full of mountains and deep valleys, high-filled cut-and-cover tunnels (HFCCTs) not only satisfy transportation demands, but they create usable land as well. Several studies have been conducted to investigate the feasibility of HFCCTs, but the time-dependent behavior of the significant backfill needed for HFCCTs has not been adequately examined. Settlement can be severely underestimated due to the time-dependent behavior of ultra-high backfill, and the earth pressure becomes redistributed accordingly. Therefore, the ability to predict the long-term behavior of backfill on HFCCTs is necessary to ensure the long-term safety of the structure. Using a discrete element method (DEM), the changes in vertical earth pressure (VEP), vertical displacement, and load transfer mechanisms above an HFCCT were investigated in this study under scenarios with and without considering backfill creep. The results show that the differential displacement of the soil and the surface settlement obviously increase due to creep and the subsequent cycles of primary and secondary consolidation. Moreover, the stress surrounding the HFCCT is redistributed, causing both the stress concentration and slope effect to weaken over time, but the VEP increases significantly. The micromechanical parameters also change correspondingly. Our results clearly show that the creep of high backfill soil must be considered carefully in HFCCT projects to ensure structural safety.