The model results demonstrated that ISWs, generated from the Lombok Strait, presented different characteristics on three stages, i.e., with the amplitude of 90 m, 50 m and 40 m on the generation, propagation and shoaling processes (
Figs 2b,
d and
f). Maximum ISW amplitudes mainly occurred at the water depth between 150 m to 400 m, covering the submarine’s collapse depth of ~200 m, thereby dragging it down to a more dangerous depth. At 21:30 UTC on 20 April 2021, an ISW packet with a leading wave amplitude of 40 m was shoaling and passing the shipwreck site (
Fig. 2f). This time is in coincidence with the reported missing time. The ISW packet had a long characteristic width of approximately 50 km and remained fluctuations for over 10 h. Even though the following waves have relatively small amplitudes of 10−30 m, the continuous wave motions are likely to have a sustained impact on the submarine (
Fig. 3). It is noteworthy that the future submarine motion should be more careful when passing the Lombok Strait (Stage 1), where the local ISWs might have a reasonably large amplitude of 90 m (
Fig. 2b) in the ocean interior. In future, when submarines sail across the Lombok Strait, the voyage depths would be better in the upper 150 m, where the ISW amplitudes are relatively small, so the ISW is unable to drag the vessel down to a dangerous depth.