Continental epithermal ore deposits are commonly associated with sedimentary organic matter, oils or solid bitumen. These organics embedded in mineral deposits can convey valuable information of the ore genesis. However, the extent to which the formation of ore minerals was recorded by organic compounds remains largely unknown, as also is how metal-rich ores interfere with the molecular proxies in the temperature regime envisaged for hydrothermal activity. The molecular compositional changes of various polycyclic aromatic steranes and polycyclic aromatic hydrocarbons and compounds derived from the Jinding Pb/Zn deposit, SW China provide new data. Aliphatic regular steranes are present as traces. The transformation from polycyclic aromatic steranes to unsubstituted polycyclic aromatic hydrocarbons is observed to show an increased trend with increasing hydrothermal alteration levels; this is consistent with the transformation from unsubstituted polycyclic aromatic hydrocarbons to heterocyclic compounds. Dehydrocyclization (aromatization) of polycyclic biological compounds and hydrodecyclization (dearomatization) of polycyclic aromatic compounds are two important reaction pathways in hydrothermal systems with moderate temperature. This detailed investigation of organic-inorganic interactions of two groups of polycyclic compounds with metal-rich ores provides insights into the questions on how and to what extent the formation of Pb/Zn deposits can be recorded by organics. This work will improve our understanding of carbon reduction, oxidation or condensation in the deep Earth and the carbon exchange between the Earth’s crust and mantle, and may shed light on the processes for ultra-deep hydrocarbon exploration.