Japan consists of many islands. From the point of view of disaster prevention, it is also important to improve the precision of strong ground motion prediction for the islands. The Ryukyu Islands are a typical example of such islands. In this study we build a 3D numerical structure model for modeling of strong ground motion, which includes land and ocean-bottom topographies and a seawater layer as well as subsurface structures of the arc side and the PHS slab, partially based on the existing models for near-surface structure and a slab-top depth of the PHS. We then try to improve the near-surface structure model in the islands using the microtremor surveys we conducted originally in this project. We then simulate seismic wave propagation for three sub-oceanic earthquakes which occurred near the Amami Islands, Okinawa Island and Miyako Island to confirm the applicability of the constructed structure model.