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[Display omitted] • A dense seismic array deployed 18 days is used to image a 3D Vs model. • Three LVZs are revealed in the shallow crust beneath the Shiziyang Waterway area. • Three cross-cutting fault zones in the sedimentary basement are identified. • Two-stage differential fault movements dominated the opening of the Shiziyang Waterway. The Shiziyang Waterway, located in the northern continental margin of the South China Sea, has developed a complex fault system owing to the coupling action of the oceanic crust and continental crust. However, the geological structure in the shallow crust beneath the Shiziyang Waterway and the relationship between faults and waterway development are still unclear, resulting in difficulty in assessing the earthquake risk to the surrounding cities. In this study, based on a high-density short-period seismic array that was recently deployed around the Shiziyang Waterway, a high-resolution shear wave velocity model is inverted to as shallow as 4 km by the ambient noise tomography method. The results showed that at depths ranging from 0.2 to 4 km, three sets of low-velocity zones (LVZs), trending east–west, northeast, and northwest, are revealed, which are speculated to be the Shougouling fault (SGLF), Xinhui-Shiqiao fault (XSF), and Shiziyang fault bundle (SZYFb), respectively. The shear-wave velocity anomalies illustrate that the SGLF stopped extending east at the north endpoint of the Wenchong-Zhujiangkou fault (WZF). The two-stage differential vertical movements of the WZF, Nangang-Humen fault (NHF), and Hualong-Haioudao fault (HHF) dominated the opening of the Shiziyang Waterway. This study provides new seismological evidence of the opening process for the Shiziyang Waterway and reveals that internal fault activity dominated the development and evolution of the Pearl River Delta. [ABSTRACT FROM AUTHOR]