The safety of the geotechnical environment around subways is vitally important for their sustainability. Ground settlement is a very common threat to the safe operation of subways and is related to subway traffic vibrations. Taking Nanjing subway line 10 as an example, field tests, discrete element simulations, and a grey relational analysis are carried out to study the deformation mechanism of the underlying sandy soil induced by vibrations. The results show that the vibration load of Nanjing subway Line 10 is mainly concentrated in the vertical direction. The particles’ coordination number below the subway increases under the vibration load, while the coordination number on the side of the tunnel decreases, which may cause a shear dilatancy effect. Among the five microscopic indexes, the local porosity and the coordination number are closely related to the deformation. Although the deformation of the underlying sandy soil is quite small under the subway traffic load, it will accumulate under frequent loading and then lead to urban engineering geological disasters.