A thick accretionary wedge with low seismic velocity overlying a subducting plate is an important factor affecting the amplitudes and durations of long‐period ground motions for great offshore earthquakes. We performed a series of 3D long‐period ground‐motion simulations to obtain a better understanding of the effects of the accretionary wedge along the Nankai trough, Japan. The simulation results demonstrate that the accretionary wedge has the effect of decreasing the peak amplitude and velocity response but amplifying and elongating later phases of long‐period ground motions in the land area. These effects depend significantly on the focal depth and are pronounced for shallow seismic sources. The amplified and elongated later phases originate mainly from prominent basin‐induced surface waves excited near the trough axis. We also identified hard sediments with intermediate S‐wave velocity in the accretionary wedge as a key layer that enhances the propagation of long‐period ground motions from offshore to onshore. In the case of the Nankai trough, the hard sediments allow long‐period ground motions developed inside the accretionary wedge to be efficiently transmitted outward in the longer period than ∼10 s. Comparisons between the observed and simulated records suggest that for more accurate predictions of long‐period ground motions, velocity structure models of not only the accretionary wedge but also the surrounding upper crust should be validated and revised using seafloor observations.