Abstract: In this study, the fatty acid compositions in the surface sediments collected from the Clarion-Clipperton Zone of the East Pacific Ocean during the 45^th and 50^th cruise were determined by gas chromatography-mass spectrometry (GC-MS). The source of sediment fatty acid and the distribution characteristics of microbial community structure were analyzed based on the variability of fatty acids in the Clarion-Clipperton Zone. Results showed that bacteria and fungi were the main sources of the sediment fatty acid in the studied area indicated by saturated fatty acids dominated by C11:0, C14:0 anteiso and C16:0, monounsaturated fatty acids by C17:1 ω7c and polyunsaturated fatty acid by C18:3 ω6c (6,9,12), respectively. The proportion of C16:0 was the highest among all stations, with a range of 9.27%-30.17%, followed by C14:0 anteiso, with a range of 4.43%-20.34%. Cluster analysis and principal component analysis showed that the fatty acid compositions in the contract areas of China Ocean Mineral Resources Research and Development Association (COMRA) and China Minmetals Corporation (CMC) were generally similar, but greater variability of fatty acid compositions were found in the CMC contract area. Water depth and particulate organic carbon fluxes may account for the geographic differences in fatty acids in the studied area, which may also be affected by the bottom flow and fine-scale topography on the seafloor.