The Doushantuo Formation (DST) in South China preserved significant bio- and chemostratigraphic records that are critical to the study of Ediacaran life and environment. Abundant microfossils and organic matter (Corg) were preserved in the DST nodules. We investigated the mineralogy, petrography and the structural characteristics of Corg in three different types (Type I: silica-rich; Type II: pyrite-rich; Type III: barite-rich) of DST nodules, in order to better understand the geobiological processes during the formation of nodules and the taphonomic details of Corg preserved therein. According to Raman spectral parameters, the Corg experienced low-grade metamorphism, and represents obvious heterogeneities of structural order and H:C in the center, rim and the host rock, respectively. Furthermore, the structural characteristics of Corg show distinct bias to various mineral matrices (silica, pyrite, goethite and barite) where they were preserved, probably due to differential mineral-organic interactions during the formation of different nodules. These mm- and μm-scale structural heterogeneities of Corg reflect the nature of precursor organism, which were subsequently affected by various post-depositional processes. Our study proposes the possible formation processes of three types of DST nodule, suggests the geobiological influences on the Corg preserved therein, and sheds light on the geobiological signatures from the DST using Raman-based approaches.