Guangdong Province in the central Cathaysian Block has two world-class metallogenic belts, namely, the Nanling and Southeastern Coastal Metallogenic Belts (NLMB and SCMB), which are spatially coincide with the major regional Ganjiang and Zhenghe-Dapu Fault Zones (GJFZ and ZDFZ). However, what roles the faults played in mineral deposition and magmatism is unclear. Using ambient noise tomography, we obtain a 3-D whole-crust shear wave velocity model. By combining available regional geophysical models, we characterize the architecture of the regional shallow lithosphere and infer its possible tectonic connection to magmatic sources, pathways and surface deposition. The results show that the study area is loosely divided by the two major faults, the GJFZ and ZDFZ, into distinct velocity domains. In the north high Vs and low Vp/Vs crust in the NLMB imply crustal remelting, which leads to the general felsic composition. In the coastal area, the lower crustal high Vs anomaly is attributed to upwelling melts associated with Cretaceous magmatic activity. Between mineral belts, a swath of crustal low-velocity zones extend into the uppermost mantle, manifesting partial melting related to upwelling magmas that may hint at a deep origin of magma from subcrustal lithosphere and likely feed surface mineral deposits through major faults. Secondary NW-trending faults coincide with low velocities and facilitated magmatic migration. A correlation between coastward extension of low velocities and younging of the Jurassic and Cretaceous magmatism is suggestive of a combined effect of slab rollback and a change in the direction of the Paleo-Pacific subduction system. We speculate a regional fault-control model in the central Cathaysian Block for the spatial-temporal evolution of regional deformation and magmatism during the middle Mesozoic.