The Gaoping (GP) river which has the largest drainage basin and is the second longest river in Taiwan. Highly erodible sedimentary and metamorphic rocks in the drainage basin, coupled with a steep landscape, humid climate, frequent typhoons and earthquakes, provide favorable conditions for bedrock weathering and soil erosion in the GP drainage basin. Its exceptionally high sediment yield and tidal-dominated dispersal system presents a unique case for comparative study. In this study, we collected sediment and soil samples not only from estuary region but also traced up to upper stream areas of the GP drainage. We analyze the content of n-alkanes in the sediments and soils of GP river-sea system, and utilize compositional patterns to discuss the sources and process of transmission of terrigenous organic matter of GP river-sea system. Analyzed results show that the average carbon chain distribution shows same pattern for rocks, riverine and seafloor sediments but is different with soil samples. Hierarchical cluster analysis helps us to distinguish differently compositional patterns of n-alkanes. And the riverine, seafloor and rock samples have high similarity, except for soils. The spatial distribution of the carbon preference index (CPI) and temporal distribution of CPI in cores, show that values are all close to ~1, but not for soils (>2). This result indicates that for the past 150 years, lower CPI values not merely from petroleum pollutions, but also due to thermal mature terrestrial organic matter eroded from bedrock caused by tectonic and climatic events, such as typhoons and earthquakes.