Abstract: Inter-story isolation is an effective method to improve the seismic performance of buildings built on top of metro depots (i.e., large chassis). To identify the factors controlling the critical design indexes and guide the detailed design, 12 study cases were designed based on a real engineering project, which includes two inter-story isolated towers built on top of a metro depot. Among these cases, three schemes and four schemes were considered for the tower and isolation system, respectively. Based on a refined model, the influence of the stiffness ratio between the tower, the isolation system and the large chassis and the yield ratio of the isolation system on nine critical design indexes were analyzed. The design indexes include the horizontal seismic absorbing coefficient (β) under the design basis earthquake, maximum inter-story drift ratio (θ_max) and maximum absolute floor acceleration (a_max) under the maximum considered earthquake of towers and chassis, maximum displacement of isolation system (D_max), maximum and minimum compressive stresses of the isolator under the maximum considered earthquake. Subsequently, the factors controlling each index were identified. For the tower, the stiffness and yield ratio of the isolation system are the controlling factors for the β and a_max. The decrease of these two factors can achieve a good control effect, while the increase of the stiffness of the tower can control β and a_max to a certain extent. The increase of the stiffness of the tower and the decease of the stiffness and the yield ratio can control θ_max to a certain extent, but such a control effect tends to stabilize when these two factors reach a certain extent. For the chassis, the schemes of the tower and isolation system has little impact on the design indexes. For the isolation system, the controlling factors for D_max are the stiffness and yield ratio of the isolation system. The decrease of these factors leads to a significant increase of D_max. The stiffness of the tower is the controlling factor for the maximum compressive stress of the isolators because the gravity increases with the stiffness. The increase of the stiffness of the tower and the decrease of the stiffness of the isolation system can significantly control the tensile stress of the isolators, and the control effect caused by the increase of the stiffness of two is more significant. The results provide a reference for the seismic performance control and design of inter-story isolated buildings built on top of metro depots.