We present a high‐resolution shear‐wave velocity model of the upper‐middle crust beneath the Pearl River Delta. The sedimentary basins are characterized by low‐velocity anomalies at depths of 6–8 km and reflect the lateral migration of the deposition centers. High‐velocity structures are located predominantly in Hong Kong, and outline the supervolcano conduit and magma reservoir in the crust. We observe contrasting velocity structures across the Lianhuashan fault zone (LFZ) where low‐velocity anomaly zones (LVZs) are developed in different strikes. Microseismic swarms at depths of 8–16 km mainly occurred at the intersection of the LVZs. Metamorphic fluids and migration in the crust are proposed to interpret the seismic activity. The intersecting LVZs would increase the lithologic permeability to allow deep‐rooted fluids to flow up, whereas the overlying high‐velocity structures representing the overflowing magma act as a permeable barrier that confines the seismicity in the middle‐lower crust. We anticipate that the detailed subsurface structures will help correlate magmatic remnants with the distribution of intraplate earthquakes and assess the earthquake risks in the Greater Bay Area of China.