The long-period strong ground motions with periods above 1 s have, in the case of farther or deeper earthquakes, potential to cause serious damage to structures with low eigen frequency, such as long bridges, oil tanks, or artificially damped structures, such as high-rise buildings. This work focuses on wave propagation due to the deep large earthquake representing rare deep damaging events of the region, with relatively sparse data coverage, studied for simple geological models computed by 2D finite differences. We model the wave propagation by finite differences using up-to-date 3D structural model of the Osaka basin. The strong surface waves in the region are not directly generated by these deep sources, but they originate by refraction mostly at the edges of the bedrock–sediments interface. The objective of this research is to model observed surface Love wave generated in the eastern part of the basin that propagates approximately westwards and is recorded by several surface stations. At these stations, the 3D finite-difference modeling provides a good fit with the observed surface wave in terms of waveform, amplitude, and arrival time for the most detailed 3D velocity model that contains topmost 50–250 m structure with the lowest S-wave velocities of 250 m/s. The semblance analysis of the synthetic wave field reveals that the respective synthetic surface wave is a result of interfering waves arriving in OSA and WOS stations from NE and SE directions. Performed tests reveal that such a synthetic wave field is extremely sensitive to the presence of the superficial 50—250 m thick low-velocity structure which is only a small fraction of the propagating surface wave length and occupies only part of the surface area. The ability to model the surface wave in terms of amplitude and time arrival validates the 3D structural model for long-period Osaka Bay earthquake scenario computations. Graphical Abstract: [Figure not available: see fulltext.] © 2023, The Author(s).