To improve the efficiency of conventional isolation trench and lighten the impact of the excavation on neighbor buildings, a novel high damping isolation trench is proposed. The viscoelastic braces equipped in the high damping isolation trench can dissipate the energy of ground-borne vibration while providing supporting force to ensure the stability of the soil on both sides. According to two actual ancient buildings, two types of high damping isolation trenchs with the plane shape of U and L are designed to solve the potential damages caused by long-term train-induced vibration. First, three-dimensional finite/infinite models based on these two buildings are established, respectively. Then, the energy dissipation characteristics are obtained by experiments. Through calculation, the control effects of the high damping isolation trenchs for these two buildings are investigated. The results indicate that the viscoelastic braces possess high energy dissipation capacity. After setting the high damping isolation trenchs around the structures, even at a small excavation depth, the acceleration and velocity responses of the two buildings are reduced significantly. Furthermore, the selected U-shaped and L-shaped trenches also show superiority compared with the conventional linear-shaped trench in this project.