Detection of hidden faults and sedimentary layers in the urban subsoil is significant for the utilization of the underground space, earthquake hazard mitigation, and so forth. Guilin, located in southwest China, is well known for the development of the most typical karst landform in the world and has become an international tourist city that needs scientific planning and knowledge of the urban underground space. After collecting waveform data recorded continuously over a period of about 1.5 months by a dense array of 114 short‐period seismic stations installed in and around Guilin, we adopt ambient seismic noise cross‐correlation method to extract Rayleigh‐wave phase velocity dispersion curves within the period range from 0.5 to 5 s and to obtain a high‐resolution S‐wave velocity (VS) model of the shallow crust above 9 km using surface‐wave tomography. The vertical VS gradient image indicates that the sediment thickness of the Guilin Karst basin is about 1–3 km. Sedimentary layers are relatively thick between Yanshan Mountain and Haiyang Mountain, and along the Yi river valley, where karst groundwater may be abundant and used as an important option for urban water supply. Both the absolute VS velocity image and the relative VS anomaly image clearly reveal the occurrence, location, and deep extension characteristics of major faults. Longsheng–Yongfu, Nanning–Guilin, Yaoshan–Yanshan, Baishi, and Guanyang–Hengyang may be regional deep faults cutting through the upper crust at least. The evolution of the basin is mainly controlled by the steep dipping Longsheng–Yongfu and Baishi faults, and partially controlled by the gently dipping Nanning–Guilin fault in the interior of the basin. The Nanning–Guilin fault is an active and partially buried fault obliquely crossing Guilin city. Urban seismic imaging, such as the new VS tomography presented here, can play an important role in understanding tectonic and tectonic‐subsidence earthquake hazards associated with these buried faults.

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