The Zhongdian arc is an important mineral province in southwest China that hosts significant Cu- and Mo-rich ore deposits. These are mainly present as Late Triassic porphyry Cu ± Mo-Au and Late Cretaceous porphyry Mo deposits, both with surrounding base metal enrichments in associated skarn, greisen, and vein occurrences. To help assess Mo resource potential in the arc-related magmatic–hydrothermal systems, we evaluated geochemical data from 1831 stream sediment samples that were collected at a density of one sample per 2 km² during the Chinese National Geochemical Mapping Program. Singularity analyses were combined with factor analysis and singularity-quantile methods to interpret distribution patterns for 18 ore-related elements and to define geochemical signatures in the stream sediment data related to areas of high favorability for the presence of Cu- and Mo-dominant ores in the Zhongdian arc. The known mineral occurrences in the arc show spatial-frequency singularity. Spatial patterns in the sediment data indicate the Triassic Cu-dominant systems are associated with intrusions emplaced along a northwest-trending system of faults, whereas the Cretaceous Mo-rich ore systems are related to north–south striking structures. The patterns indicate locations of high favorability for new discoveries of Mo occurrences in the central part of the arc where many deposits are already known, as well as in the southwestern part of the arc that presently lacks abundant known occurrences. Factor analysis results show that the areas favorable for the Mo porphyries are best defined by a Mo–W–Bi–Pb–Ag signature in the sediment data. These can be distinguished from areas most likely to contain older Cu-rich systems that are marked by sediments with Cu, Zn, and Au anomalies. The singularity analysis, in combination with factor analysis and singularity-quantile, was able to successfully separate anomalies in the sediment samples that were representative of the Late Triassic and Late Cretaceous mineral systems, despite elements such as Mo, Pb, and Ag being enriched in ores of both ages.