The vertical distributions of bulk and molecular biomarker compositions in the samples from four sediment cores of the Changjiang (Yangtze River) Estuary were determined. The changes in the bulk and molecular compositions with depth suggest that there have been recent changes in the marine autogenic and terrigenous supply. In the site at the boundary of the turbidity maximum (Site 8) and the most southern site (Site 26), the autogenic and allochthonous inputs make almost the same contribution to sedimentary organic matter. In the site close to the river mouth (Site 11), the organic matter mainly comes from the terrestrial input carried by the Changjiang water, whereas, in the most eastern site (Site 17), the organic matter consists of a mixture of recent and ancient Changjiang delta sedimentary residues. Significant downcore fluctuations were observed in the patterns of the bulk and molecular compositions, as well as in several biomarker ratios, which also indicates the different anoxic conditions at different depths of the core besides the source variation. In addition, the distributions of molecular compounds show that the organic matter is a mixture of immature and mature in the sediments of the four cores, which further indicates that the microbial activity is active in anoxic conditions, especially in the surface sediment. The vertical distributions of molecular compounds also show that the autogenic marine organic matter is more easily degraded, and that the molecular compounds evolve from unstable steric configurations to stable ones in the early diagenetic processes.