The Luotuodun archaeological site is located in Yixing City, Jiangsu Province, in the transition zone from the Yili Mountains to the coastal plain. It is of Neolithic Age and dates from approximately 7000 to 5000 years ago. A large number of animal skeleton fossils have been unearthed at the site, many of which, especially those belonging to species of Cervidae (possibly Sika, Cervis nippon), are characterized by the presence of black residue on the surface. There are three types of residue, one is black film-like coating, which is suggestive of exposure to fire, one is also black, but crystalline in nature, while the other is grey-white, particulate deposit. With the aim of exploring the nature of these residues and their possible origins, we applied a number of analytical techniques, including Raman Spectroscopy (RS), Fourier Transform Infrared Spectroscopy (FTIR), Energy dispersive spectroscopy (EDS) and Electron Microscopy (EM) on six bone fossils belonging to different parts of Cervidae skeleton unearthed from Luotuodun to evaluate the possible influence of fire and/or depositional processes in their formation. The black film-like coating, widespread on the surface of these bones, is highly reflective and appears white under the Raman microscope. The RS peak indicates that the film-like substance is rich in carbonaceous (graphitic carbon) components, suggesting that the bones have been exposed to combustion. FTIR measurements on these bones show that the structure of hydroxyapatite carbonate (Ca10(PO4)6−x(CO3)x(OH)2) has changed, consistent with their exposure to very high temperatures (500–600 °C), and implying that they were burnt, either for cooking or ritual behavior by ancient humans. In the case of the crystallized black particles, these are primarily confined to localities on the surface of bone fractures. EDS results, as confirmed by the RS analysis, show that the black crystals are comprised of an iron-rich, phosphatic mineral, compatible with vivianite (Fe3(PO4)2·(H2O)8). The substantial vivianite content is consistent with the fossil bones being submerged and deposited in waterlogged soils. The results of EDS show that the composition of the grey-white particle is hydroxyapatite carbonate (Ca10(PO4)6−x(CO3)x(OH)2). Non-destructive geochemical analysis of the surface residues of these Luotuodan bones provides valuable evidence for reconstructing the taphonomy of the Cervidae bones, and reveals that they were utilized by ancient humans during the Luotuodun culture period in SE China.