The southern part of the Ailaoshan-Red River shear zone (ARRSZ) in southern Yunnan, is an important gold-bearing polymetallic metallogenic belt of China. To better understand the metallogenic tectonic setting and the magmatic activity in the area, we deployed a 240-km-long quasi-linear seismic array with numerous short-period stations spaced about 500 m across the ARRSZ. The shear-velocity structure of the upper crust along the survey profile is determined by ambient noise tomography using continuously recorded waveform data. The results show: (1) An upper crust characterized by a laterally varying S-velocity pattern and two high velocity bodies: one located mainly below the Ailaoshan metallogenic belt and the other further east below the Pingbian area, which are separated by a low velocity zone beneath the Red River Fault. (2) The upper crust model provides valuable information on Cenozoic magmatism. The high-velocity body below the Ailaoshan metallogenic zone likely corresponds to buried granitoid intrusions caused by early-stage Cenozoic magmatism, which might have been altered and mineralized. The high-velocity body near Pingbian could be the trace of basalt-generating late-stage Cenozoic magmatism, which is most likely the intrusive phase of the younger basalts. (3) Major regional faults are identified as ascending channels and/or emplacement/precipitation sites for magma and mineralized fluids, meaning that such faults play an ore-controlling function within the magmatic fluid ore-formation system.