The sedimentary basins of East Siberia are among Russian most significant hydrocarbon-bearing basins, with the Vendian Nepa complex being a primary exploration target. Despite confirmed hydrocarbon reserves, full-scale development faces delays due to complex geological structures. Exploitation of these reserves is challenged by lithological heterogeneity, arising from facies variability and post-sedimentary transformations. Thus, facies and paleogeographic reconstructions, along with the study of structural-textural rock features and mineral composition, are crucial. This research aims to investigate the lithological composition and reservoir properties to address geological complexities and improve hydrocarbon extraction efficiency. To achieve these goals, we employed a new research methodology involving multi-scale lithological, petro-physical, and geophysical studies. These included detailed core sample analyses of structure, texture, granulometry, and mineral composition using diffractometry and laboratory express analyzers. The pore space structure was examined via optical electron microscopy, and CT scans were interpreted for component models. Additionally, well logging and 2D/3D seismic survey data were interpreted using acoustic inversion technology. Laboratory core studies identified paragenetic rock associations formed under specific hydrodynamic conditions. Facies analysis considered post-glacial continental settings and early Vendian climatic changes, revealing significant impacts on reservoir structure. Sectors with low-porosity, poorly permeable heterogeneous sandstones, dolomite, and anhydrite lenses were localized in well sections. Post-sedimentary processes were observed in wells in tectonically active sectors near major faults. Seismic prediction, based on acoustic properties, mapped zones favorable for reservoir rock formation. Studying structural and mineral characteristics, and identifying lateral and vertical distribution patterns, refined the geological model. This enhances exploratory drilling success in East Siberia.