Hydropower development has increased the degree of fragmentation of riparian habitats and the problem of reservoir sediment trapping. However, there is limited research on the source and distribution characteristics of organic matter (OM) in river reservoirs. Therefore, the migration mechanisms of OM in reservoirs remain unclear. In this study, the lipid biomarker analysis method was applied to surface sediments of Pubugou Reservoir in Dadu River. Sediment OM lipid components were analysed by gas chromatography-mass spectrometry (GC-MS), and were quantified and classified into four sources: natural, petrogenic, pyrogenic and sewage markers. The results showed that the average content of organic matter (OM) in the upstream area of the dam (10.7%±4.8%) was higher than that in the downstream area of the dam (7.3%±0.9%) and within the reservoir (6.7%±1.8%), indicating the impact of reservoir interception on the accumulation of sedimentary OM. The extractable lipid fraction was mainly derived from natural markers (45.9%±13.9%). The OM was represented by the relative ratio of carbon preference index, terrestrial/aquatic ratio and terrestrial/aquatic plant input ratio. It came mainly from terrestrial higher plants, accounting for 70.5%±9.1% of the natural quantitative molecules. In addition, the number of anthropogenic marker molecules increased significantly (44.6%±25.1%) compared to natural markers (24.2%±3.7%) at sites downstream of the dam in Hanyuan. Further proportion studies revealed the contribution of sewage markers (31.6%±12.8%) due to the low coverage of domestic sewage treatment plants in the residential area. Our study provides a certain theoretical basis for the coupling effect between the compositional change of OM pollution sources and the retention effect of the reservoir.