Distinguishing biomineralized minerals from inorganic minerals has been a longstanding challenge. The organic matter within biomineralized minerals constitutes compelling evidence that sets them apart from inorganic minerals. However, for small samples that have undergone degradation and diagenetic alteration, routine analytical technologies have difficulties in identifying internal residual organic signals. Atom Probe Tomography, as the highest-spatial-resolution microanalytical technique, facilitates the study of elements spatial distribution and nano-scale structures, holding significant potential for applications in biogeochemistry. In this study, Atom Probe Tomography has been applied to fossil samples for the first time, comparing inorganic Durango apatite with fossil conodont. This research discovered residual organic components within conodont, manifesting in the form of nano-scale particles coupled with high carbon and nitrogen concentrations. This signal is promising for differentiating between biominerals and inorganic minerals, which is greatly potential for identifying nano-scale biosignatures in ancient samples.