Abstract: In order to study the origin of organic matter and phytoplankton community structure of marine sediments in Zhoushan, the non-polar matter and intact phospholipids composition in the sediment cores at 23 sites of the Daishan, Hengshan and Shengsi islands was examined by GC-MS and UPLC-MS. The study showed that the sediments organic material in the Zhoushan was derived from both terrestrial plants and marine organism, of which terrestrial inputs were about 60% and marine inputs were about 40%. The range of the ratio of high to low carbon hydrocarbon (∑T/∑M) was between 0.54 and 2.73, and the high ∑T/∑M value area was close to Hangzhou bay, the low ∑T/∑M value area was near the coastal of the East China sea. Compared with the Yangtze estuary area, Zhoushan sediment was less affected by terrestrial input, but much higher than the tide-frequent-occurrence area in the East China Sea. The content of Phosphatidylglycerol in sediments was higher than the Phosphatidylethanolamine and Phosphatidylinositol, the fatty acid parameter ∑C₁₆/∑C₁₈ was near 1. These results indicated that the main Phytoplankton in the sediments of Zhoushan was microalgae, and dinoflagellates and diatoms had no special advantages.