Biomarkers, commonly regarded as molecular fossils, preserve structural information inherited from their biological precursors and thus provide important evidence for tracing the sources, transformation, and environmental significance of sedimentary organic matter. In estuarine and coastal settings, where natural inputs and human disturbances are often superimposed, the molecular composition of sediments provides a useful archive for understanding regional differences in organic matter accumulation and alteration. In this study, sediments from ten functionally distinct estuarine and coastal environments spanning tropical to polar regions were comparatively investigated. The distributions of hydrocarbons and related compounds showed clear regional differences in molecular composition. Aromatic hydrocarbons were more pronounced in regions under stronger human influence, whereas long-chain alkanes, sterols, hopanes, and terpenoid-related compounds were more characteristic of environments receiving stronger natural organic matter inputs. High-latitude sediments were further marked by prominent unresolved complex mixtures and distinctive compound assemblages, indicating specific pathways of organic matter alteration. Overall, this study highlights the value of biomarker-based molecular characterization for revealing regional heterogeneity in sedimentary organic matter and provides a comparative basis for interpreting source inputs and early transformation processes in complex coastal environments.