The Northern Jiangsu-South Yellow Sea is underlain by the Yangtze Craton continental lithosphere. Based on the collected phase velocity data of Rayleigh surface wave, a depth inversion of the underground three dimensional S wave velocity structure in the Northern Jiangsu-South Yellow Sea area was carried out. Based on the data, the relationship between the geological structure and seismotectonics of the Northern Jiangsu-South Yellow Sea Basin was discussed. The surface wave tomography results show that the regional velocity structure model is basically consistent with the geological characteristics of the study area, and the velocity structure clearly depicts the main sedimentary structure range and basement fluctuation of the Northern Jiangsu-South Yellow Sea Basin. The inversion results also reveal that there is a remarkable low velocity layer in the middle crust of the Northern Jiangsu-South Yellow Sea Basin, which is consistent with the concentrated distribution area of historically strong earthquakes, indicating that the activity of shallow strong earthquakes is closely related to the low velocity layer in the crust.