The Fuzhou basin is an ideal place for high-resolution paleoclimate study due to its special location (in the coastal zone), where sediments recorded a wealth of information on the interaction between ocean and land during the Holocene. In this paper, rock magnetism, environmental magnetism and paleomagnetism features of core FZ5 sediments in the Fuzhou basin were studied to reveal response of magnetic properties to terrigenous input, sea-level change and diagenesis. The rock magnetism results show that ferrimagnetic minerals with low coercivity are the dominant minerals, while the types of magnetic minerals vary in different stages of environmental variation. Magnetite, siderite and some amounts of Fe-sulphides are the main contributors to magnetic properties in the transgression environment during the early and middle Holocene (9 similar to 3 cal. ka BP), although sulphidation dissolved fine-grained magnetite to form greigite and pyrite. However, sulphidation did not completely eliminate the natural remanence carried by magnetite and the dominant controls of the terrestrial detritus input and sea-level fluctuations to magnetic properties in this stage. During the late Holocene (3 cal. ka BP), magnetite was still partly dissolved to greigite due to the earlier reduction in the terrestrial oxidizing environment, but further transformation was restrained by the oxidation then. Strong oxidation process formed the high coercivity minerals and disturbed the natural remanence. During the deposition process, the six strong ancient oxide interfaces were produced at similar to 8.2, similar to 7.7, similar to 7.5, similar to 2.7, similar to 1.5, similar to 0.5 cal. ka BP, respectively, reflecting the unusually dry or humid climate events in the Fuzhou basin over these times.