As a new emerging seismic method for delineating subsurface structure, the potential of ambient noise tomography (ANT) is investigated for mineral deposit targeting at the exploration scale. This passive seismic technique is used to image the subsurface 3D S-wave velocity of the Caosiyao porphyry molybdenum deposit in the North China Craton. Intriguingly, the key structures of this giant porphyry mineral system down to the depth of 2 km are characterized by distinct S-wave velocity anomalies, with ore deposition sites and fluid pathways (faults) characterized by distinct velocity lows, whereas fluid drivers (granites) generate velocity highs. The 3D S-wave velocity anomalies, along with seismic reflection profile and potential field data, allow us to delineate the deep-seated ore-controlling structures such as fault systems, granitic plutons, and even ore deposition sites under thickly covered sediments in the study area. The results suggest that the occurrence of the Caosiyao ore deposit is closely related to the huge amount of magma fluid intruding along the channel of the Datong-Shangyi fault at a depth of >2 km. Our study demonstrates that the ANT technique has the accuracy and resolution needed for mineral exploration targeting at the deposit scale, with a relatively lower environmental impact as well as lower cost than active-source seismology.