Abstract: After the impoundment of the Three Gorges Reservoir in 2003, shallow earthquakes occurred frequently, which had a great impact on local productions and lives. The study of shallow velocity structure is of great significance for shallow seismic disaster assessment and disaster prevention and reduction in Zigui area. In this paper, based on the vertical component continuous waveform records of 24 mobile seismic stations in Zigui area of Hubei Province from June to July of 2020, the empirical Green’s functions between the stations are obtained by cross-correlation of the ambient seismic noise, the Rayleigh wave group velocity dispersion curves on the period 0.6−5 s are extracted, and the inversion for the three-dimensional S-wave velocity model is obtained within 6 km near the surface of the region. The results show that the S-wave velocity of Zigui basin and its south adjacent area is significantly lower than that of the eastern fault area, which is consistent with the structural evolution and sedimentary characteristics of different structural blocks in the studied area; an earthquake with M_S4.2 occurred on the vertical high-velocity and low-velocity junction area of the study area in 2014. The S-wave velocity decreases obviously near the Yangtze River region in the fault zone, indicating that the Yangtze River water penetrates into the fault area. Therefore, the frequent occurrence of earthquakes in Zigui area is related to the water load and water infiltration of the Three Gorges reservoir.