In nature, minerals record various origins and information for geology and geobiochemistry. Here, we investigated the origin of organic matter and growth mechanism of quartz with oil inclusion revealing fluorescence under short ultraviolet (UV) light, obtained from the clay vein at Shimantocho, Kochi, Shikoku Island, Japan. Geological investigation indicated that the oil−quartz was formed in hydrothermal metamorphic veins found in the late Cretaceous interbedded sandstone and mudstone. The obtained oil−quartz crystals are mostly double-terminated. Micro-X-ray computed tomography (microCT) indicated that oil−quartz crystals have various veins originating as skeleton structures along the quartz crystal {111} and {1−11} faces. Spectroscopic and chromatographic studies indicated that aromatic ester and tetraterpene (lycopene) molecules, which revealed fluorescence, were detected. Large molecular weight sterol molecules, such as C40, were also detected in the vein of oil−quartz. This investigation indicated that organic inclusions in mineral crystals would form with ancient microorganism culture environments.