In this paper, a series of 1-g shaking table model tests were carried out to investigate the seismic behavior of a relatively stiff rectangular tunnel structure installed in soft clay bed, accounting for different ground motions with varying peak accelerations. Using a validated numerical analysis procedure, a suite of three-dimensional (3D) finite element (FE) analyses was performed to systematically study the factors of tunnel burial depth, seismic intensity, flexural rigidity of the middle column and tunnel wall thickness on the seismic response of rectangular tunnel structures installed in clayey ground. It was found that, with the increasing burial depth, the seismic response of rectangular tunnel structure became more intense due to the increased inertial force arising from the overlying clay; in terms of improving the seismic performance of tunnel structure, increasing tunnel wall thickness seemed more effective than increasing flexural rigidity of the middle column. Furthermore, it was found that the existing simplified approaches generally tended to overestimate the earthquake-induced racking distortions of rectangular tunnels installed in clayey ground. A new semi-empirical relationship was derived for better correlating the racking ratio with flexibility ratio for rectangular tunnels embedded in soft clays, which could provide a useful reference for the seismic design and risk assessment of similar clay-tunnel systems.