Organic carbon isotopes in sediments have been frequently used to identify the source of organic matter. Here we present a study of organic δ13C on two sediment profiles influenced by guano from Guangjin and Jinqing islands in the Xisha Archipelago, South China Sea. Organic matter from ornithogenic coral sand sediments has two main sources, guano pellets and plant residues, and their organic δ13C (δ13COM) are significantly different. Organic carbon δ13Cguano is much higher than δ13Cplant, and δ13COM of bulk samples is intermediate. Based on a two-end-member mixing model, the proportions of guano- and plant-derived organic matter in the bulk samples were reconstructed quantitatively. The results showed that seabirds began to inhabit the islands around approximately 1200–1400 AD, and that guano pellets have been an important source of soil organic matter since then. With the accumulation of guano-derived nutrients, plants began to develop prosperously on the islands in the last 200 years, which is reflected by the significant increase of plant-derived organic matter in the upper sediment layer. However, guano-derived organic matter decreased greatly in recent decades, indicating a rapid decrease in seabird population. Our results show that organic δ13C can be effectively used to quantitatively determine different source contributions of OM to bulk ornithogenic coral sand sediments.